Comprehensive cancer predisposition testing within the prospective MASTER trial identifies hereditary cancer patients and supports treatment decisions for rare cancers.

BACKGROUND: Germline variant evaluation in precision oncology opens new paths toward the identification of patients with genetic tumor risk syndromes and the exploration of therapeutic relevance. Here, we present the results of germline variant analysis and their clinical implications in a precision oncology study for patients with predominantly rare cancers. PATIENTS AND METHODS: Matched tumor and control genome/exome and RNA sequencing was carried out for 1485 patients with rare cancers (79%) and/or young adults (77% younger than 51 years) in the National Center for Tumor Diseases/German Cancer Consortium (NCT/DKTK) Molecularly Aided Stratification for Tumor Eradication Research (MASTER) trial, a German multicenter, prospective, observational precision oncology study. Clinical and therapeutic relevance of prospective pathogenic germline variant (PGV) evaluation was analyzed and compared to other precision oncology studies. RESULTS: Ten percent of patients (n = 157) harbored PGVs in 35 genes associated with autosomal dominant cancer predisposition, whereof up to 75% were unknown before study participation. Another 5% of patients (n = 75) were heterozygous carriers for recessive genetic tumor risk syndromes. Particularly, high PGV yields were found in patients with gastrointestinal stromal tumors (GISTs) (28%, n = 11/40), and more specifically in wild-type GISTs (50%, n = 10/20), leiomyosarcomas (21%, n = 19/89), and hepatopancreaticobiliary cancers (16%, n = 16/97). Forty-five percent of PGVs (n = 100/221) supported treatment recommendations, and its implementation led to a clinical benefit in 40% of patients (n = 10/25). A comparison of different precision oncology studies revealed variable PGV yields and considerable differences in germline variant analysis workflows. We therefore propose a detailed workflow for germline variant evaluation. CONCLUSIONS: Genetic germline testing in patients with rare cancers can identify the very first patient in a hereditary cancer family and can lead to clinical benefit in a broad range of entities. Its routine implementation in precision oncology accompanied by the harmonization of germline variant evaluation workflows will increase clinical benefit and boost research.

Phylogeny of the order Phyllachorales (Ascomycota, Sordariomycetes): among and within order relationships based on five molecular loci.

The order Phyllachorales (Pezizomycotina, Ascomycota) is a group of biotrophic, obligate plant parasitic fungi with a tropical distribution and high host specificity. Traditionally two families are recognised within this order: Phyllachoraceae and Phaeochoraceae, based mostly on morphological and host characteristics. Currently, the position of the order within the class Sordariomycetes is inconclusive, as well as the monophyly of the order, and its internal phylogenetic structure. Here we present a phylogeny of the order Phyllachorales based on sequence data of 29 species with a broad host range resulting from a wide geographical sampling. We inferred Maximum Likelihood and Bayesian phylogenies from data of five DNA regions: nrLSU rDNA, nrSSU rDNA, ITS rDNA, and the protein coding genes RPB2, and TEF1. We found that the order Phyllachorales is monophyletic and related to members of the subclass Sordariomycetidae within Sordariomycetes. Within the order, members of the family Phaeochoraceae form a monophyletic group, and the family Phyllachoraceae is split into two lineages. Maximum Likelihood ancestral state reconstructions indicate that the ancestor of Phyllachorales had a monocotyledonous host plant, immersed perithecia, and a black stroma. Alternative states of these characters evolved multiple times independently within the order. Based on our results we redefine the family Phyllachoraceae and propose the new family Telimenaceae with Telimena erythrinae as type species, resulting in three families in the order. Species of Telimena spp. occur in several monocotyledonous and eudicotyledonous host plants except Poaceae, and generally have enlarged black pseudostroma around the perithecia, a character not present in species of Phyllachoraceae.

Nonadherence to anti-tuberculosis treatment, reasons and associated factors among pulmonary tuberculosis patients in the communities in Indonesia.

BACKGROUND: Tuberculosis (TB) is the world's major public health problem. We assessed the proportion, reasons, and associated factors for anti-TB treatment nonadherence in the communities in Indonesia. METHODS: This national coverage cross-sectional survey was conducted from 2013 to 2014 with stratified multi-stage cluster sampling. Based on the region and rural-urban location. The 156 clusters were distributed in 136 districts/cities throughout 33 provinces, divided into three areas. An eligible population of age ≥15 was interviewed to find TB symptoms and screened with a thorax x-ray. Those whose filtered result detected positive followed an assessment of Sputum microscopy, LJ culture, and Xpert MTB/RIF. Census officers asked all participants about their history of TB and their treatment-defined Nonadherence as discontinuation of anti-tuberculosis treatment for <6 months. Data were analyzed using STATA 14.0 (College Station, TX, USA). RESULTS: Nonadherence to anti-TB treatment proportion was 27.24%. Multivariate analysis identified behavioral factors significantly associated with anti-TB treatment nonadherence, such as smoking (OR = 1.78, 95% CI (1.47-2.16)); place of first treatment received: government hospital (OR = 1.45, 95% CI:1.06-1.99); private hospital (OR = 1.93, 95% CI: 1.38-2.72); private practitioner (OR = 2.24, 95% CI: 1.56-3.23); socio-demographic and TB status included region: Sumatera (OR = 1.44, 95% CI: 1.05-1.98); other areas (OR = 1.84, 95% CI: 1.30-2.61); low level of education (OR = 1.60, 95% CI: 1.27-2.03); and current TB positive status (OR = 2.17, 95% CI: 1.26-3.73). CONCLUSIONS: Nonadherence to anti-TB drugs was highly related to the personal perception of the respondents, despite smoking, current TB status, a place for the first treatment, education, and region. The position of the first TB treatment at the private practitioner was significantly associated with the risk of Nonadherence to treatment.

Tackling the Challenge of Extracting Microplastics from Soils: A Protocol to Purify Soil Samples for Spectroscopic Analysis.

Microplastic pollution in soils is an emerging topic in the scientific community, with researchers striving to determine the occurrence and the impact of microplastics on soil health, ecology, and functionality. However, information on the microplastic contamination of soils is limited because of a lack of suitable analytical methods. Because micro-Fourier-transform infrared spectroscopy (µ-FTIR), next to Raman spectroscopy, is one of the few methods that allows the determination of the number, polymer type, shape, and size of microplastic particles, the present study addresses the challenge of purifying soil samples sufficiently to allow a subsequent µ-FTIR analysis. A combination of freeze-drying, sieving, density separation, and a sequential enzymatic-oxidative digestion protocol enables removal of the mineral mass (>99.9% dry wt) and an average reduction of 77% dry weight of the remaining organic fraction. In addition to visual integrity, attenuated total reflectance FTIR, gel permeation chromatography, and differential scanning calorimetry showed that polyamide, polyethylene, polyethylene terephthalate, and polyvinyl chloride in the size range of 100 to 400 µm were not affected by the approach. However, biodegradable polylactic acid showed visible signs of degradation and reduced molecular weight distribution after protease treatment. Nevertheless, the presented purification protocol is a reliable and robust method to purify relatively large soil samples of approximately 250 g dry weight for spectroscopic analysis in microplastic research and has been shown to recover various microplastic fibers and fragments down to a size of 10 µm from natural soil samples. Environ Toxicol Chem 2022;41:844-857. © 2021 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.

Isolated progressive visual loss after coiling of paraclinoid aneurysms.

BACKGROUND AND PURPOSE: The proximity of the paraclinoid segment of the internal carotid artery to the visual pathways may result in visual deficits when patients present with aneurysms in this segment. Although surgical clip ligation of these aneurysms has been the standard of care for decades, the advent of coil embolization has permitted endovascular therapy in those aneurysms with favorable dome-to-neck ratios. Although immediate nonprogressive visual loss after coil embolization of paraclinoid aneurysms has been well described, isolated progressive visual loss immediately or shortly following coil embolization, to our knowledge, has not. We have identified 8 patients who experienced progressive loss of vision, unassociated with any other neurologic deficits, developing immediately or shortly after apparently uncomplicated coil embolization of a paraclinoid aneurysm. MATERIALS AND METHODS: This study is a retrospective case series of 8 patients seen at 4 separate academic institutions. Inpatient and outpatient records were examined to determine patient demographics, previous ocular and medical history, and ophthalmic status before endovascular embolization. In addition, details of the primary endovascular therapy and subsequent surgical and nonsurgical interventions were recorded. Follow-up data, including most recent best-corrected visual acuity, postoperative course, and duration of follow-up were documented. RESULTS: Eight patients developed progressive visual loss in 1 or both eyes immediately or shortly after apparently uncomplicated coiling of a paraclinoid aneurysm. MR imaging findings suggested that the visual loss was most likely caused by perianeurysmal inflammation related to the coils used to embolize the aneurysm, enlargement or persistence of the aneurysm despite coiling, or a combination of these mechanisms. Most patients experienced improvement in vision, 2 apparently related to treatment with systemic corticosteroids. CONCLUSION: Patients in whom endovascular treatment of a paraclinoid aneurysm is contemplated should be warned about the potential for both isolated nonprogressive and progressive visual loss in 1 or both eyes. Patients in whom progressive visual loss occurs may benefit from treatment with systemic corticosteroids.

Myc is an essential negative regulator of platelet-derived growth factor beta receptor expression.

Platelet-derived growth factor BB (PDGF BB) is a potent mitogen for fibroblasts as well as many other cell types. Interaction of PDGF BB with the PDGF beta receptor (PDGF-betaR) activates numerous signaling pathways and leads to a decrease in receptor expression on the cell surface. PDGF-betaR downregulation is effected at two levels, the immediate internalization of ligand-receptor complexes and the reduction in pdgf-betar mRNA expression. Our studies show that pdgf-betar mRNA suppression is regulated by the c-myc proto-oncogene. Both constitutive and inducible ectopic Myc protein can suppress pdgf-betar mRNA and protein. Suppression of pdgf-betar mRNA in response to Myc is specific, since expression of the related receptor pdgf-alphar is not affected. We further show that Myc suppresses pdgf-betar mRNA expression by a mechanism which is distinguishable from Myc autosuppression. Analysis of c-Myc-null fibroblasts demonstrates that Myc is required for the repression of pdgf-betar mRNA expression in quiescent fibroblasts following mitogen stimulation. In addition, it is evident that the Myc-mediated repression of pdgf-betar mRNA levels plays an important role in the regulation of basal pdgf-betar expression in proliferating cells. Thus, our studies suggest an essential role for Myc in a negative-feedback loop regulating the expression of the PDGF-betaR.

Promotion of growth and apoptosis in c-myc nullizygous fibroblasts by other members of the myc oncoprotein family.

c-myc nullizygous fibroblasts (KO cells) were used to compare the abilities of c-myc, N-myc and L-myc oncoproteins to accelerate growth, promote apoptosis, revert morphology, and regulate the expression of previously described c-myc target genes. All three myc oncoproteins were expressed following retroviral transduction of KO cells. The proteins all enhanced the growth rate of KO cells and significantly shortened the cell cycle transition time. They also accelerated apoptosis following serum deprivation, reverted the abnormal KO cell morphology, and modulated the expression of previously described c-myc target genes. In most cases, L-myc was equivalent to c-myc and N-myc in restoring all of the c-myc-dependent activities. These findings contrast with the previously reported weak transforming and transactivating properties of L-myc. Myc oncoproteins may thus impart both highly similar as well as dissimilar signals to the cells in which they are expressed.

Nosocomial acquisition of beta-lactamase--negative, ampicillin-resistant enterococcus.

BACKGROUND: A recent prospective study at the Department of Veterans Affairs Medical Center, Martinez, Calif, revealed that 9% of enterococcal clinical isolates were ampicillin resistant. We prospectively studied 100 patients hospitalized in one general medicine ward and in the medical intensive care unit to study determinants of acquisition of ampicillin-resistant enterococcus. METHODS: Rectal swabs and urine cultures were obtained from patients within 72 hours of admission to the study ward and twice weekly until discharge from the ward or the intensive care unit. Cultures were obtained from the hands of personnel and from environmental surfaces in the general medical ward and the intensive care unit. Ampicillin-resistant enterococcal isolates were examined for molecular relatedness by plasmid DNA analysis. RESULTS: The cultures from 23 patients yielded ampicillin-resistant enterococci. The rectal swabs yielded ampicillin-resistant enterococci before the urine cultures did except in one patient whose urine and rectal cultures were both positive on the same day. Acquisition of ampicillin-resistant enterococci was significantly associated with previous antimicrobial agents, Foley catheterization, and being bedridden. Resistant enterococci were not isolated from hospital personnel or environmental surfaces. Plasmid analysis by gel electrophoresis demonstrated nine strains, two of which predominated. Rectal and urine isolates from the same patient had identical plasmid electrophoresis patterns. CONCLUSIONS: We conclude that ampicillin-resistant enterococci are common in the rectal flora, can spread to the urinary system, are associated with patient characteristics that predipose to nosocomial infection, and may become an emerging clinical problem.

Current recommendations and future prospects in the treatment of toxoplasmosis.

Toxoplasma infection is highly prevalent throughout the world and causes disease in diverse populations. Effective treatment regimens are available for each clinical entity of toxoplasma, but problems of incomplete clinical efficacy, drug potency, drug safety, and length of treatment remain. No well-controlled clinical trials in humans have been performed to evaluate the efficacy and safety of treatment. Primary treatment of toxoplasmosis is with the synergistic combination of pyrimethamine and sulphonamide. This is considered the treatment of choice for severe disease, disease in immunocompromised patients, and congenital toxoplasmosis. Spiramycin, a macrolide antibiotic, is frequently used alone or alternately with pyrimethamine and sulphonamide for pregnant women with the acute acquired infection to prevent congenital toxoplasmosis. Clindamycin is used frequently to treat acute flares of toxoplasmic chorioretinitis and as second-line therapy for toxoplasmic encephalitis in patients with the acquired immunodeficiency syndrome (AIDS). Inadequacies in the treatment of toxoplasmosis in immunosuppressed patients, exemplified by experience with AIDS patients, should provide the impetus for well-designed trials to find and evaluate more potent and better-tolerated agents. Classes of new drugs that have been investigated and show some promise include: (a) macrolides (roxithromycin, azithromycin); (b) folic acid antagonists (piritrexim and trimetrexate), and (c) purine analogues (arprinocid). Immunomodulators have attracted interest, and interferon-gamma alone and in combination with roxithromycin is effective in murine models. Interleukin-2 is also effective in the murine model.

Six billion neurons lost in AIDS. A stereological study of the neocortex.

Human immunodeficiency virus type 1 (HIV1) is neurotropic. One of the morphological changes that is seen in patients with acquired immunodeficiency syndrome (AIDS) is cerebral atrophy affecting various structures including the neocortex. The cause of atrophy is not known. The total number of neocortical neurons was estimated in formalin fixed brains of 12 males with AIDS and 12 male controls matched for age and height. The mean number of neocortical neurons was 16.0 x 10(9) (coefficient of variation = 0.11) in the AIDS patients compared with 21.9 x 10(9) (coefficient of variation = 0.22) in the controls, a difference of approximately six billion (p < 0.005, 2-tailed). The global neuronal loss was 37%, and affected all four neocortical lobes. Ten patients did not have a history of central nervous system symptoms; two patients had a history of dementia. The number of neurons in the AIDS cases was not associated with dementia. AIDS is the first disease in which a global loss of neocortical neurons has been demonstrated using unbiased stereological methods. The loss of more than one third of the neurons may partly explain the cortical atrophy. Focal neuron loss has been reported by several authors, but none have been based on unbiased methods. In this group of AIDS patients the severe loss of neurons did not correspond to neurological deficits.

Connecting the eye to the brain: the molecular basis of ganglion cell axon guidance.

In the past several years, a great deal has been learnt about the molecular basis through which specific neural pathways in the visual system are established during embryonic development. This review provides a framework for understanding the principles of retinal ganglion cell axon guidance, and introduces some of the families of axon guidance molecules involved. In addition, the potential relevance of retinal axon guidance to human visual developmental disorders, and to retinal axon regeneration, is discussed.

Schwartz-Bartter's syndrome and mesencephalic astrocytoma.

A case of an astrocytoma arising in the mesencephalon is reported. The patient was first treated at the age of 11 years. He led a normal life for almost 20 years and survived for 25 years in spite of a recurrence 14 years after the initial operation. The last couple of years he developed various neurological disorders and a Schwartz-Bartter's syndrome. The clinical picture is explained by the growth of the tumor along the neuraxis to the hypothalamus.

Plasminogen activator in vaginal smears during the menstrual cycle.

A cytologic staining technique in which the reaction produces an insoluble colored precipitate at the site of trypsin-like proteolysis was applied to human vaginal smears, taken daily over six menstrual cycles. The day of urinary LH surge for each cycle was determined. The enzyme action, namely hydrolysis by plasminogen activator, is confined mainly to intermediate squamous cells. The number of cells stained by the enzyme method reaches a maximum three days prior to the LH surge, whereas the maximum in karyopyknosis occurs close to or at the day of LH surge. The enzyme staining method can thus be used when anticipation of ovulation by about 4 days is needed. No immediate fixation is required prior to the enzyme staining.

Morphology of tracheal scar after resection with CO2-laser and high-frequency cutting loop. A study in normal pigs.

In 6 pigs a bronchoscopical resection of the tracheal mucosa was performed using CO2-laser on one side, and an electric high-frequency cutting loop (ECL) on the other. The pigs were sacrificed 3 months later. On macroscopic examination the tracheal mucosa appeared almost normal on the laser-resected side, while severe deformation was seen after ECL treatment. Microscopically the respiratory epithelium had regenerated irrespective of the instrument used. After laser resection the subepithelial tissue had a normal width and consisted of collagen fibrils with few vessels and sparse fragmented elastic tissue. The cartilage showed necrosis and pericellular fibrosis. The scar tissue after ECL was a broad cellular and richly vascularized connective tissue. The content of elastic fibres was markedly greater than after laser resection. The cartilage showed small irregular necroses lined by pyknotic nuclei. In neither case had the gland regenerated. Both CO2-laser and ECL caused severe (but not identical) damage to the tissue, clearly visible after 3 months. However, the deformation caused by ECL was not seen at the laser-resected sites, which makes the laser technique seem preferable--where economy permits.

[Toxoplasma encephalitis with atypical manifestation and normal CT]. / Toxoplasma-encephalitis med atypisk manifestation og normal CT.

A case of cerebral toxoplasmosis in a HIV-positive man with unusual clinical manifestations and a normal computed tomographic (CT) scanning is presented. Even though most patients with cerebral toxoplasmosis have focal neurological deficits on physical examination, the patients can also present with more diffuse symptoms. Neither the lack of antitoxoplasma antibodies nor normal findings at CT scanning exclude the diagnosis of toxoplasma encephalitis. The sensitivity is higher with magnetic resonance than with CT scanning. We present a case story that demonstrate how delusive cerebral toxoplasmosis can be in HIV positive patients. It is recommended that the possibility of cerebral toxoplasmosis be considered in every HIV-positive patient with neurological symptoms and empirical therapy be instituted on wide indications.