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Phylogenetic analysis of ecomorphological divergence, community structure, and diversification rates in dusky salamanders (Plethodontidae: Desmognathus).

An important dimension of adaptive radiation is the degree to which diversification rates fluctuate or remain constant through time. Focusing on plethodontid salamanders of the genus Desmognathus, we present a novel synthetic analysis of phylogeographic history, rates of ecomorphological evolution and species accumulation, and community assembly in an adaptive radiation. Dusky salamanders are highly variable in life history, body size, and ecology, with many endemic lineages in the southern Appalachian Highlands of eastern North America. Our results show that life-history evolution had important consequences for the buildup of plethodontid-salamander species richness and phenotypic disparity in eastern North America, a global hot spot of salamander biodiversity. The origin of Desmognathus species with aquatic larvae was followed by a high rate of lineage accumulation, which then gradually decreased toward the present time. The peak period of lineage accumulation in the group coincides with evolutionary partitioning of lineages with aquatic larvae into seepage, stream-edge, and stream microhabitats. Phylogenetic simulations demonstrate a strong correlation between morphology and microhabitat ecology independent of phylogenetic effects and suggest that ecomorphological changes are concentrated early in the radiation of Desmognathus. Deep phylogeographic fragmentation within many codistributed ecomorph clades suggests long-term persistence of ecomorphological features and stability of endemic lineages and communities through multiple climatic cycles. Phylogenetic analyses of community structure show that ecomorphological divergence promotes the coexistence of lineages and that repeated, independent evolution of microhabitat-associated ecomorphs has a limited role in the evolutionary assembly of Desmognathus communities. Comparing and contrasting our results to other adaptive radiations having different biogeographic histories, our results suggest that rates of diversification during adaptive radiation are intimately linked to the degree to which community structure persists over evolutionary time.

Adaptation, Biological↗

[Hemorrhage caused by cerebral arterial aneurysm].

The analysis of clinical pictures and pathomorphology of cerebral damage (intra-operative and autopsy material) was performed on 387 patients with first or second rupture of cerebral arterial aneurysms. Clinicopathological peculiarities of the aneurysmic intracranial hemorrhages were derived. Intracranial pathomorphological determinants of the severity of the patients' conditions at the acute stage were determined, including the intracerebral hematomas resulting in dislocation syndrome and paving the way to penetration of arterial blood spring into the ventricles on the second rupture of the aneurysm. The clinical course of the condition featured a stabilization period whose duration depended on both the type of hemorrhage and cerebral response. This period was regarded as optimal for reconsidering an option of surgical intervention.

Acute Disease↗

[Merits of interureteral anastomosis in the treatment of unilateral extensive non-neoplastic lesions of the pelvic ureter in adults].

The authors intend to set out the merits of interureteral anastomosis for unilateral extensive lesions of the pelvic ureter. In order to achieve a good homogeneity on one hand and a greater distance in time (8 and 12 years in two cases) on the other hand, they decided to confine their study to the non-neoplastic lesions of adult patients, which are most often iatrogenic. This brief analysis shows that interureteral anastomosis is simpler than ureteroileoplasty when ureterovesical plasty is impossible (psoic, bladder tubulization). Contrary to a widespread opinion, itl does not seriously jeopardize the receiving, ie. normal, urinary tract. The chances of salvage of the initially threatened upper urinary tract are considerable (at least 75 to 80%). The production of an ureteroureteral reflux is a negligible risk, as is the spread of an infection towards the normal kidney. Of course, these good results can be achieved only with an accurate, minutious procedure, of which the authors describe the essential features. The stability of the results is confirmed by the long period elapsed in some cases.

Aged↗

Glucagon antagonists: contribution to binding and activity of the amino-terminal sequence 1-5, position 12, and the putative alpha-helical segment 19-27.

Glucagon binding to and recognition by its cell surface receptor is the necessary first step in the cascade of events leading to the activation of adenylate cyclase by the hormone. It has long been presumed that glucagon adopts an ordered conformation upon binding to its membrane-bound receptor. A recent model of this three-dimensional structure based on biophysical data, predicts beta-turns at positions 2-5, 10-13, and 15-18, and an alpha-helical region between residues 19-27. Our approach in the design of antagonists of glucagon was to elucidate the steric and electronic features that stabilize these secondary structures to obtain analogs that bind with high affinity to the receptor but do not activate adenylate cyclase. Nineteen glucagon analogs incorporating structural changes at the amino-terminal sequence 1-5, at positions 9 and 12, and at the carboxyl-terminal helical region were synthesized. Des-His1-[Glu9]glucagon amide was recently shown to be a competitive inhibitor. Our synthetic studies in combination with this modification have resulted in seven new glucagon antagonists. The implications for the structural and conformational properties required for binding and activity of glucagon and the glucagon peptide family are discussed.

Adenylyl Cyclases↗

Differential contributions of two elements of rho-independent terminator to transcription termination and mRNA stabilization.

The hallmark features of rho-independent transcription terminators are a G(+)C-rich dyad symmetry sequence followed by a run of T residues on a sense strand. Both of these structural elements are required for efficient transcription termination. Besides its primary function, rho-independent terminators are also known to enhance expression of an upstream gene by stabilizing RNA in a few cases. The Escherichia coli crp gene encoding cAMP receptor protein (CRP) contains a typical rho-independent terminator. To gain further insight into the roles of the G(+)C-rich dyad symmetry sequence and the poly(T) tract both in transcription termination and mRNA stabilization, we constructed a series of variant crp terminators and analyzed their abilities regarding these two functions. Disruption of the G(+)C-rich dyad symmetry sequence almost completely eliminated terminator activity while disruption of the poly(T) tract reduced terminator activity significantly but not completely. Thus, the contribution of the G(+)C-rich dyad symmetry sequence to transcription termination is larger than that of the poly(T) tract. Disruption of the G(+)C-rich dyad symmetry region reduced expression of the upstream crp gene by accelerating the rate of mRNA degradation. However, disruption of the poly(T) sequence had no effect on the stability of the crp mRNA, indicating that the poly(T) tract plays no role in mRNA stabilization. When the crp terminator was replaced by terminators derived from other genes, the fusion genes expressed the crp mRNA at the same level as did the native crp gene, suggesting that the mRNA stabilization effect is probably a general nature of rho-independent terminators.

Bacterial Proteins↗

Early onset psychotic disorders: diagnostic stability and clinical characteristics.

OBJECTIVES: To examine the clinical features and diagnostic stability of early-onset psychotic disorders. METHODS: These data are from a two-year longitudinal prospective study of youth with psychotic disorders. Standardized diagnostic assessments are administered at baseline and at one and two-year's follow-up. RESULTS: Fifty-one subjects have been recruited to date; 18 with schizophrenia, 14 with bipolar disorder, 7 with schizoaffective disorder, 1 with an organic psychosis, and 11 subjects whose symptoms where either questionable and/or did not meet diagnostic criteria for another disorder (classified as psychosis nos). Thirty-nine subjects were reassessed at year one, twenty-four at year two. Three subjects have been lost to follow-up. The study diagnosis was the same as the first onset diagnosis (prior to entering the study) in 50% of subjects. Over the two-year period of the study, the diagnosis remained unchanged in over 90% of subjects. Subjects with schizophrenia had higher ratings of premorbid impairment, including social withdrawal and dysfunctional peer relationships, than those with bipolar disorder. At the one-year follow-up, subjects with schizophrenia and schizoaffective disorder had significantly higher rates of delusions, bizarre behavior, and negative symptoms than those with bipolar disorder. Subjects with bipolar disorder tended to have cyclical courses, whereas those with schizophrenia and schizoaffective disorder were often chronically impaired. Subjects with psychosis nos had higher rates of dissociative symptoms and histories of child maltreatment. CONCLUSIONS: Early-onset psychotic disorders can be reliably diagnosed using standardized assessments and are stable over a two-year period. Compared to bipolar disorder, schizophrenia is associated with a poorer premorbid history, and persistent positive and negative symptoms.

Adolescent↗

Stability distribution in the phage lambda-DNA double helix: a correlation between physical and genetic structure.

Statistical analyses on the positional correlation of physical-stability and base-sequence distribution maps with genetic map are made for the whole DNA (48502 bases) of lambda-phage. The susceptibility to a double-helix unfolding perturbation and the fraction of the transient opening of a particular region of the double helix are adopted to define this physical stability. The principal features obtained are: A) The DNA double strand of protein coding regions is found to have homostabilizing propensity around a defined stability which is characteristic to each individual gene. B) The stability of the double helix in non-protein coding region fluctuates, on average over the whole region, more than that in protein coding region. C) Boundary regions of protein coding and non-protein coding regions are regions of high stability-fluctuation. Stability especially fluctuates at the protein-coding-region side of the boundary. Contrary to the quiet feature of the interior part of protein coding region rather noisy part exists at its edge. D) One frequently opening region coincides with the attaching site for the site specific recombination between phage and bacterial DNA. There are two possible ways to explain the noisy feature in the stability distribution in non-protein coding regions: 1) The region has been used as the locus of recombination as evolution took place. Thus DNAs which were homostabilized around a different value characteristic to each individual DNA, have been joined there many times, so that the noise has accumulated as a remnant of evolutional history; and/or 2) the base-composition homogenizing or double-helix homostabilizing mechanism does not work in unneeded region such as non-protein coding region or introns. Since corresponding characteristics have been found in our previous analyses on other viral and globin-gene DNAs, the rules mentioned above may be comprehensively extended to other DNAs.

Bacteriophage lambda↗

Linking MRI radiomics to transcriptomics-based radiosensitivity in lower-grade glioma: A radiogenomic framework.

BACKGROUND: RSI is a transcriptomics-based biomarker associated with radiotherapy outcomes, but its clinical application is constrained by the requirement for tumor tissue and RNA sequencing. This study investigates whether MRI-derived radiomic features can reflect RSI-defined intrinsic radiosensitivity in lower-grade glioma.This addresses a critical gap arising from the limited availability of matched imaging and genomic data in routine clinical practice. METHODS: MRI-derived radiomic features were extracted from FLAIR images of lower-grade glioma patients obtained from TCIA and matched with transcriptomic data from TCGA. A total of 107 patients with both MRI and RNA sequencing data were included in the radiogenomic analysis. Radiomic features were ranked using a Borda-based ensemble feature selection strategy. Five supervised machine-learning classifiers were trained to predict RSI-based radiosensitivity classification, and model interpretability was assessed using SHAP within radiogenomic framework. RESULTS: Classification performance increased with feature number and stabilized at compact subset of 13 radiomic features. Logistic regression showed stable performance with an AUC of 0.82 (95 % CI: 0.71-0.93). SHAP analysis indicated that heterogeneity-related texture features were dominant contributors to model predictions, with many associated with the RR phenotype, while others were linked to the RS phenotype. CONCLUSION: An MRI-based radiomic signature enables non-invasive prediction of RSI-defined radiosensitivity in lower-grade glioma. Rather than offering an immediately deployable clinical tool, this study establishes a proof-of-concept radiogenomic framework demonstrating that intrinsic radiosensitivity, traditionally assessed through invasive molecular assays, can be approximated using quantitative imaging features. These findings highlight the potential of imaging-based radiosensitivity assessment and provide a foundation for future radiogenomic investigations.

Lower-grade glioma↗

Muonic helium atom as a classical three-body problem

We study the classical problem of the muonic helium atom, a helium atom with one of its electrons replaced by a muon. First, we establish the connection of the model with the one-dimensional frozen planetary approximation of the helium atom and find that there is classically stable motion for the configuration alpha-particle-electron-muon, and no stable motion for the alpha-particle-muon-electron configuration. After that, we introduce the restricted muonic helium problem, a model for the movement of an electron in the potential of the alpha particle/muon pair moving in a circular orbit. In this model, the equilibrium points, their associated Lyapunov families of periodic orbits, and their stability parameters were studied. The most interesting feature is the stability of the halo orbits, for a range of energy values. The vicinity of the alpha particle is also studied, examining Poincare sections for increasing energy values showing an increase of the chaotic motion.

Journal Article↗

Hyperthermostable protein structure maintained by intra and inter-helix ion-pairs in archaeal O6-methylguanine-DNA methyltransferase.

The crystal structure of O6-methylguanine-DNA methyltransferase (EC 2.1.1.63) of hyperthermophilic archaeon Pyrococcuskodakaraensis strain KOD1 (Pk -MGMT) was determined by single isomorphous replacement method with anomalous scattering (SIRAS) at 1.8 A resolution. The archaeal protein is extremely thermostable and repairs alkylated DNA by suicidal alkyl transfer from guanine O6 to its own cysteine residue. Archaea constitute the third primary kingdom of living organisms, sharing characteristics with procaryotic and eucaryotic cells. They live in various extreme environments and are thought to include the most ancient organisms on the earth. Structural studies on hyperthermophilic archaeal proteins reveal the structural features essential for stability under the extreme environments in which these organisms live, and will provide the structural basis required for stabilizing various mesophilic proteins for industrial applications. Here, we report the crystal structure of Pk-MGMT and structural comparison of Pk-MGMT and methyltransferase homologue from Escherichia coli (AdaC, C-terminal fragment of Ada protein). Analyses of solvent-accessible surface area (SASA) reveals a large discrepancy between Pk-MGMT and AdaC with respect to the property of the ASA. In the Pk-MGMT structure, the intra-helix ion-pairs contribute to reinforce stability of alpha-helices. The inter-helix ion-pairs exist in the interior of Pk-MGMT and stabilize internal packing of tertiary structure. Furthermore, structural features of helix cappings, intra and inter-helix ion-pairs are found around the active-site structure in Pk-MGMT.

Amino Acid Sequence↗

Postnatal development of a large auditory nerve terminal: the endbulb of Held in cats.

The endbulbs of Held are formed by the ascending branches of myelinated auditory nerve fibers and represent one of the largest synaptic endings in the brain. Most of the developmental changes in structure occur during the first 30 postnatal days of age. The neonatal endbulb begins as a flattened expansion with many filopodia, resembling a growth cone and characterized by numerous puncta adherentia and synapses associated with small postsynaptic densities; the most impressive feature of the ending at this age is its highly irregular plasma membrane that interdigitates with that of the postsynaptic spherical bushy cell. During these first 30 days, the number of puncta adherentia diminishes, postsynaptic densities nearly double in size, intermembraneous cisternae emerge, and plasma membranes flatten. These features endow the endbulb with an adult-like appearance. On the other hand, synaptic vesicle density increases progressively from approximately 50/microm2 at birth to 100/microm2 at adulthood. Mitochondria size remains constant over this developmental period but mitochondrial volume fraction increases until 60 days postnatal. Although many features of endbulb morphology stabilize by 30 days, other features suggest that endbulb development continues into the third month of age. Many of these observations correlate with the maturation of physiological response properties and suggest issues for further study.

Aging↗

Depression with versus without manic features in rapid-cycling bipolar disorder.

Depression has been identified as a hallmark feature of rapid-cycling bipolar disorder, although less attention has been paid to the presence of manic features accompanying depression in rapid cyclers. To provide greater information about the extent to which depression arises with or without salient manic features in rapid cycling, we conducted a preliminary study of rapid cycling in outpatients seeking treatment at an academic specialty center for bipolar disorder. Forty DSM-IV affectively symptomatic bipolar outpatients with past year DSM-IV rapid cycling underwent systematic evaluation of symptoms and illness characteristics. Manic and depressive symptoms, treatments, and clinical features were rated by standardized scales. Major depression was present in most rapid cyclers (85%), but salient manic features were also evident in half of all depressed rapid cyclers. A lifetime history of suicide attempts was significantly more common in rapid cyclers who presented with major depression plus salient manic features than in those who presented with pure depression or pure mania (p = .033). Antidepressants were being prescribed for approximately one third of depressed rapid cycling patients regardless of the presence of concomitant manic features, whereas mood stabilizers tended to be used less often when manic features accompanied depression. Depression in conjunction with manic symptoms, rather than pure depression alone, may be more common among rapid-cycling bipolar patients who seek treatment. Lifetime suicide risk may be greater among rapid cycling patients whose depression occurs in tandem with manic symptoms. Prescribing habits in the community that favor antidepressants over mood stabilizers may promote further mood destabilization in this population. Further studies with larger sample sizes are needed to affirm these provisional findings.

Academic Medical Centers↗

Prediction of pH-dependent properties of proteins.

We describe what may be the most accurate approach currently available for the calculation of the pKas of ionizable groups in proteins. The accuracy is assessed by comparison of computed pKas with 60 measured pKas in a total of seven proteins. The overall root-mean-square error is 0.89 pKa units. Linear regression analysis of computed versus measured pKas yields a slope of 0.95, y-intercept of -0.02 and a correlation coefficient of 0.96. The proposed approach also picks out many of the shifted pKas of groups in enzyme active sites and special salt bridges. However, it does yield several over-shifted pKas and tends to underestimate pKa shifts which result from desolvation effects. We examine the ability of the new approach to reproduce the dependence of protein stability upon pH, using the ionization polynomial formalism. Overall features of the stability curves are reproduced, but the quantitative agreement is not particularly good. The reasons for the disagreement may have to do both with insufficient accuracy in the theory and with uncertainty in the nature of the unfolded state of proteins. The methodology described here is based upon finite difference solutions of the Poisson-Boltzmann equation. Its success depends upon the use of the rather high protein dielectric constant of 20. However, theoretical considerations and the fact that pKa shifts which result from desolvation are underestimated here imply that the dielectric constant of the protein interior actually is lower than 20. We suggest that the high protein dielectric constant improves the overall agreement with experiment because it accounts approximately for phenomena which tend to mitigate pKa shifts and which are not specifically included in the model. These include conformational relaxation and specific ion-binding. Future models based upon a low protein dielectric constant and treating such phenomena explicitly might yield improved agreement with experiment.

Amino Acids↗

Functional morphology of the lemuriform wrist joints and the relationship between wrist morphology and positional behavior in arboreal primates.

A comparative study of carpal joint structure and function in six Malagasy lemuriforms was undertaken to test predicted morphoclines in carpal joint morphology between pronograde and orthograde arboreal primates. Patterns of movement at the wrist during locomotion were observed and described for the lemuriform species Lemur fulvus and Propithecus verreauxi. Lemur fulvus, which assumes a pronograde posture during locomotion, extends and pronates the wrist during the support phase of quadrupedal walking and running stride cycles. Furthermore, the forearm of this species exhibits some transverse movement across the proximal wrist joint during the support phase. In contrast, the indriid Propithecus maintains the hand and wrist in a flexed and partially supinated position during vertical clinging and suspensory postures. Habitual quadrupedal and vertical postures in Malagasy primates are in turn related to very different patterns of carpal joint morphology and articular mechanics. Those lemurs which are predominantly pronograde share a series of structural features related to stabilizing the antebrachiocarpal joint during extension and mediolateral deviation and the midcarpal joint during pronation: an intraarticular labrum is present on the inner portion of the radiocarpal ligament, the radiocarpal articular surface is quite flat dorsoventrally, the capitate-trapezoid embrasure is expanded dorsally, and development of the radial and ulnar styloids is more pronounced. The wrists of Propithecus, Avahi, and Lepi-lemur (vertical clingers) differ from those of quadrupedal lemuriforms in possessing a suite of morphological features related to stabilizing the wrist during antebrachiocarpal flexion and midcarpal supination: the radiocarpal articular surface is deeply curved and tilted anteriorly, the dorsal radiocarpal ligament is very broad, thick, and fibrous, the hamate's triquetral facet is directed proximodistally, and the capitate-trapezoid embrasure is dorsally constricted and expanded palmarly. These observed contrasts in carpal form and function are used to define further the morphological features related to orthograde posture in several lineages of arboreal primates.

Animals↗

[Testing of bacterial mutants as potential vaccine strains].

The most important expectations made on the development of live vaccines are expounded, before a certain order is proposed according to which mutants should be tested. First, the characteristic features of the mutants should be determined with high accuracy, and the stability of these features should be established by repeated tests. Testing for harmlessness should not be undertaken until in vitro stability of a given mutant is established with certainty. The problems and possibilities associated to such tests are described by examples of Escherichia coli and Salmonella mutants. Immunogenic effectiveness of a given mutant has to be verified, after the harmlessness of the same mutant has been confirmed. Actual choice for potential use as vaccine strain will have to depend primarily on the results of an active protection experiment. The results obtained from Escherichia coli, Shigella, and Salmonella mutants are compared to those recorded from inactivated antigens.

Animals↗

Variable regions V13 and V3 of Saccharomyces cerevisiae contain structural features essential for normal biogenesis and stability of 5.8S and 25S rRNA.

The homologous ribosomal RNA species of all organisms can be folded into a common "core" secondary structure. In addition, eukaryotic rRNAs contain a large number of segments, located at fixed positions, that are highly variable in size and sequence from one organism to another. We have investigated the role of the two largest of these variable regions in Saccharomyces cerevisiae 25S rRNA, V13, and V3, by mutational analysis in a yeast strain that can be rendered completely dependent on the synthesis of mutant (pre-)rRNA. We found that approximately half of variable region V13 can be deleted without any phenotypic effect. The remaining portion, however, contains multiple structural features whose disturbance causes serious growth defects or lethality. Accumulation of 25S rRNA is strongly reduced by these mutations, at least in part because they inhibit processing of ITS2. Removal of even a relatively small portion of V3 also strongly reduces the cellular growth rate and larger deletions are lethal. Interestingly, some of the deletions in V3 cause accumulation of 27S(A) pre-rRNA and, moreover, appear to interfere with the close coupling between the processing cleavages at sites A3 and B1(S). These results demonstrate that both variable regions play an important role in 60S subunit formation.

Base Sequence↗

A possible folding pathway of bovine pancreatic RNase.

A theoretical pathway for the folding of RNase into its native conformation is derived from the contact map computed from crystallographic coordinates. The pathway is based on the hypothesis of Tanaka and Scheraga, according to which localized conformations stabilized by short- and medium-range interactions form before those conformational features that are stabilized primarily by long-range interactions. The pathway deduced from the contact map agrees with experimental information on intermediates detected in the thermal unfolding of RNase and in immunochemical studies on the formation of stable antigenic sites when deduced RNase is oxidized with glutathione. Ambiguities in the interpretation of the contact map are resolved by the combination of structural information contained in the contact map and experimental information.

Amino Acid Sequence↗

Clinical analysis of anti-Ma2-associated encephalitis.

Increasing experience indicates that anti-Ma2-associated encephalitis differs from classical paraneoplastic limbic or brainstem encephalitis, and therefore may be unrecognized. To facilitate its diagnosis we report a comprehensive clinical analysis of 38 patients with anti-Ma2 encephalitis. Thirty-four (89%) patients presented with isolated or combined limbic, diencephalic or brainstem dysfunction, and four with other syndromes. Considering the clinical and MRI follow-up, 95% of the patients developed limbic, diencephalic or brainstem encephalopathy. Only 26% had classical limbic encephalitis. Excessive daytime sleepiness affected 32% of the patients, sometimes with narcolepsy-cataplexy and low CSF hypocretin. Additional hormonal or MRI abnormalities indicated diencephalic-hypothalamic involvement in 34% of the patients. Eye movement abnormalities were prominent in 92% of the patients with brainstem dysfunction, but those with additional limbic or diencephalic deficits were most affected; 60% of these patients had vertical gaze paresis that sometimes evolved to total external ophthalmoplegia. Three patients developed atypical parkinsonism, and two a severe hypokinetic syndrome with a tendency to eye closure and dramatic reduction of verbal output. Neurological symptoms preceded the tumour diagnosis in 62% of the patients. Brain MRI abnormalities were present in 74% of all patients and 89% of those with limbic or diencephalic dysfunction. Among the 34 patients with cancer, 53% had testicular germ-cell tumours. Two patients without evidence of cancer had testicular microcalcification and one cryptorchidism, risk factors for testicular germ-cell tumours. After neurological syndrome development, 17 of 33 patients received oncological treatment (nine also immunotherapy), 10 immunotherapy alone, and six no treatment. Overall, 33% of the patients had neurological improvement, three with complete recovery; 21% had long-term stabilization, and 46% deteriorated. Features significantly associated with improvement or stabilization included, male gender, age <45 years, testicular tumour with complete response to treatment, absence of anti-Ma1 antibodies and limited CNS involvement. Immunosuppression was not found to be associated with improvement but was clearly effective in some patients. Fifteen patients (10 women, five men) had additional antibodies to Ma1. These patients were more likely to have tumours other than testicular cancer and to develop ataxia, and had a worse prognosis than patients with only anti-Ma2 antibodies (two women, 21 men); 67% of deceased patients had anti-Ma1 antibodies. Anti-Ma2 encephalitis (with or without anti-Ma1 antibodies) should be suspected in patients with limbic, diencephalic or brainstem dysfunction, MRI abnormalities in these regions, and inflammatory changes in the CSF. In young male patients, the primary tumour is usually in the testis, in other patients the leading neoplasm is lung cancer.

Adult↗