Miracle-dz/UniFAR-FTUs huggingface dataset:
Malignancy in disorders of sex development

Disorders of sex development (DSD) represent a spectrum of conditions in which chromosomal, gonadal, or anatomic sex are atypical and affect 1 in 4,500–5,000 live births. The diagnosis of DSD raises concerns of tumor risk and treatment as well as future fertility preservation. We review the current understanding of the types of gonadal tumors that arise in DSD patients as well as possible markers and treatment. The goal is to inform the members of the DSD team (urologist, endocrinologist, geneticist, psychologist) of the latest findings regarding malignancy in DSD. PubMed® and Google ScholarTM literature searches were performed of current and past peer-reviewed literature on DSD (intersex) regarding gonadal development and tumor formation/treatment. Relevant reviews and original research articles were examined, including cited references, and a synopsis of the data was generated. DSD patients are at increased risk for the development of testicular carcinoma in-situ (CIS) and germ cell tumors (GCT), including seminoma, non-seminoma, juvenile granulosa cell, gonadoblastoma, and dysgerminoma. Cancer risk factors include Y-chromosomal material and gonadal position, especially for streak gonads. The 46 XX DSD patients [congenital adrenal hyperplasia (CAH)] with no genetic Y-chromosomal material are not at higher risk of cancer. Post-pubertal complete androgen insensitivity syndrome (AIS) patients remain prone to tumor development if the testes remain in the abdomen. Estimates of the risk of GCT in partial AIS for untreated undescended testes may be as high as 50%. The cancer risk of scrotal testes in partial AIS is unknown. CIS occurs almost exclusively in patients with hypovirilization, most notably in AIS. Persistent Mullerian Duct Syndrome (PMDS) confers the usual cancer risk associated with cryptorchidism, but also a possible tumor risk of the Mullerian remnant. Several markers are under investigation for tumor evaluation in the DSD population beyond hCG and AFP (Oct3/4, TSPY, WT-1). The management of patients with DSD is complex and evaluation of tumor risk is aided by advances in genotyping for Y-chromosomal material not evident in traditional karyotyping. More complete genetic screening for DSD patients should increasingly become the standard of care. Developments in pathologic diagnosis will further challenge our traditional understanding of the oncologic management and surveillance of these patients. Future studies utilizing more advanced histologic examination of gonads will improve our understanding of the true incidences of malignancy in this diverse population.
Traffic of a Viral Movement Protein Complex to the Highly Curved Tubules of the Cortical Endoplasmic Reticulum

Intracellular trafficking of the nonstructural movement proteins of plant viruses plays a crucial role in sequestering and targeting viral macromolecules in and between cells. Many of the movement proteins traffic in unconventional, yet mechanistically unknown, pathways to localize to the cell periphery. Here we study trafficking strategies associated with two integral membrane movement proteins TGBp2 and TGBp3 of Potexvirus in yeast. We demonstrate that this simple eukaryote recapitulates the targeting of TGBp2 to the peripheral bodies at the cell cortex by TGBp3. We found that these viral movement proteins traffic as an ∼1:1 stoichiometric protein complex that further polymerizes to form punctate structures. Many punctate structures depart from the perinuclear endoplasmic reticulum (ER) and move along the tubular ER to the cortical ER, supporting that it involves a lateral sorting event via the ER network. Furthermore, the peripheral bodies are associated with cortical ER tubules that are marked by the ER shaping protein reticulon in both yeast and plants. Thus, our data support a model in which the peripheral bodies partition into and/or stabilize at highly curved membrane environments.
Oxidative Stress in Gastric Mucosa of Asymptomatic Humans Infected with Helicobacter pylori: Effect of Bacterial Eradication

Background. Inducible nitric oxide synthase (iNOS) and interleukin 8 (IL‐8) are positive in approximately 50% of Helicobacter pylori‐related diseases but it is not clear whether oxidative stress is also present in H. pylori asymptomatic humans. Our aim was to study the expression of iNOS, superoxide dismutase, catalase and IL‐8 production in H. pylori‐infected asymptomatic humans, and to investigate the effect of eradication of H. pylori.
Measurement of expressive vocabulary in school-age children: Development and application of the Kilifi Naming Test (KNT)

ABSTRACT The dearth of locally developed measures of language makes it difficult to detect language and communication problems among school-age children in sub-Saharan African settings. We sought to describe variability in vocabulary acquisition as an important element of global cognitive functioning. Our primary aims were to establish the psychometric properties of an expressive vocabulary measure, examine sources of variability, and investigate the measure’s associations with non-verbal reasoning and educational achievement. The study included 308 boys and girls living in a predominantly rural district in Kenya. The developed measure, the Kilifi Naming Test (KNT), had excellent reliability and acceptable convergent validity. However, concurrent validity was not adequately demonstrated. In the final regression model, significant effects of schooling and area of residence were recorded. Contextual factors should be taken into account in the interpretation of test scores. There is need for future studies to explore the concurrent validity of the KNT further.
Emotional states recognition, implementing a low computational complexity strategy

This article describes a methodology to recognize emotional states through an electroencephalography signals analysis, developed with the premise of reducing the computational burden that is associated with it, implementing a strategy that reduces the amount of data that must be processed by establishing a relationship between electrodes and Brodmann regions, so as to discard electrodes that do not provide relevant information to the identification process. Also some design suggestions to carry out a pattern recognition process by low computational complexity neural networks and support vector machines are presented, which obtain up to a 90.2% mean recognition rate.
Effects of Sequence Composition and Patterning on the Structure and Dynamics of Intrinsically Disordered Proteins

Unlike the well defined structures of classical natively folded proteins, Intrinsically Disordered Proteins (IDP) and Intrinsically Disordered Regions (IDR) dynamically span large conformational and structural ensembles. This dynamic disorder impedes the study of the relationship between the amino acid sequences of the IDPs and their spatial structures, dynamics, and function. Multiple experimental and theoretical evidence points in many cases to the overall importance of the general properties of the amino acid sequence of the IPDs rather than their precise atomistic details. However, while different experimental techniques can probe aspects of the IDP conformations, often different techniques or conditions offer seemingly contradictory results. Using coarse-grained polymer models informed by experimental observations, we investigate the effects of several key variables on the dimensions and the dynamics of IDPs. The coarse-grained simulations are in a good agreement with the results of atomistic MD. We show that the sequence composition and patterning are well reflected in the global conformational variables such as the radius of gyration and hydrodynamic radius, while the end-to-end distance and dynamics are highly sequence specific. We identify the conditions that allow mapping of highly heterogeneous sequences of IDPs onto averaged minimal polymer models. We discuss the implications of these results for the interpretation of the recent experimental measurements, and for further development of appropriate mesoscopic models of IDPs.
Health and Street/ Homeless Youth

This article reviews the Canadian literature on health issues for homeless/street youth couched in terms of the broad determinants of health. A description of the target population is presented, followed by a discussion of the health risks associated with living in marginal and precarious situations `on the street'. In particular, the potential consequences of engaging in the risky and often dangerous activities (e.g. substance abuse and high-risk sex) associated with the street lifestyle are discussed. Key conclusions drawn from the relevant literature are taken into consideration in a final section that includes a discussion of the policy implications of this work.
Truth in Reporting: How Data Capture Methods Obfuscate Actual Surgical Site Infection Rates within a Health Care Network System

BACKGROUND: Two systems measure surgical site infection rates following colorectal surgeries: the American College of Surgeons National Surgical Quality Improvement Program and the Centers for Disease Control and Prevention National Healthcare Safety Network. The Centers for Medicare & Medicaid Services pay-for-performance initiatives use National Healthcare Safety Network data for hospital comparisons. OBJECTIVE: This study aimed to compare database concordance. DESIGN: This is a multi-institution cohort study of systemwide Colorectal Surgery Collaborative. The National Surgical Quality Improvement Program requires rigorous, standardized data capture techniques; National Healthcare Safety Network allows 5 data capture techniques. Standardized surgical site infection rates were compared between databases. The Cohen &kgr;-coefficient was calculated. SETTING: This study was conducted at Boston-area hospitals. PATIENTS: National Healthcare Safety Network or National Surgical Quality Improvement Program patients undergoing colorectal surgery were included. MAIN OUTCOME MEASURES: Standardized surgical site infection rates were the primary outcomes of interest. RESULTS: Thirty-day surgical site infection rates of 3547 (National Surgical Quality Improvement Program) vs 5179 (National Healthcare Safety Network) colorectal procedures (2012–2014). Discrepancies appeared: National Surgical Quality Improvement Program database of hospital 1 (N = 1480 patients) routinely found surgical site infection rates of approximately 10%, routinely deemed rate “exemplary” or “as expected” (100%). National Healthcare Safety Network data from the same hospital and time period (N = 1881) revealed a similar overall surgical site infection rate (10%), but standardized rates were deemed “worse than national average” 80% of the time. Overall, hospitals using less rigorous capture methods had improved surgical site infection rates for National Healthcare Safety Network compared with standardized National Surgical Quality Improvement Program reports. The correlation coefficient between standardized infection rates was 0.03 (p = 0.88). During 25 site–time period observations, National Surgical Quality Improvement Program and National Healthcare Safety Network data matched for 52% of observations (13/25). &kgr; = 0.10 (95% CI, –0.1366 to 0.3402; p = 0.403), indicating poor agreement. LIMITATIONS: This study investigated hospitals located in the Northeastern United States only. CONCLUSIONS: Variation in Centers for Medicare & Medicaid Services-mandated National Healthcare Safety Network infection surveillance methodology leads to unreliable results, which is apparent when these results are compared with standardized data. High-quality data would improve care quality and compare outcomes among institutions.
Studies on Axenfeld–Rieger syndrome patients and mice reveal Foxc1's role in corneal neovascularization

Normal vision critically depends on the transparency of the cornea overlying the lens. This tissue is made up of precisely oriented layers of fibroblasts perfectly interwoven with the collagen and other ECM components that they produce. Importantly, in the healthy eye, there are no blood vessels or lymphatic vessels in the stroma, making it what is known as an “angiogenically privileged” site. However, in a number of human ocular disorders, and in response to injuries like chemical burns, blood vessels do grow into the cornea from around the junction between the iris and the sclera (the limbus). This pathological angiogenesis can severely disrupt clarity of vision and necessitate corneal transplants. Consequently, there is intense interest in understanding the processes that normally restrict blood vessel growth into the cornea. In PNAS, Seo et al. (1) provide compelling evidence from human and mouse studies that implicate one member of the large Forkhead box (Fox) transcription factor family [Forkhead box transcription factor c1 (Foxc1)] in the regulation of corneal avascularity. Specifically, they suggest that Foxc1 regulates the normal delicate balance between factors in the cornea that can promote angiogenesis (e.g., VEGF and VEGF receptor) and those that inhibit growth of blood vessels and lymphatics (e.g., soluble VEGF receptor).
Implications of Tanoak Decline in Forests Impacted By Phytophthora ramorum: Girdling Decreases the Soil Hyphal Abundance of Ectomycorrhizal Fungi Associated With Notholithocarpus densiflorus

Abstract Invasive plant pathogens are often recognized as serious threats to the maintenance of biodiversity affecting both structure and function of ecosystems. Here, we investigate the potential impact of the invasive pathogen Phytophthora ramorum Werres, de Cock & Man in't Veld by using physical girdling of tanoak, Notholithocarpus densiflorus (Hook. & Arn.) Manos, Cannon & S. H. Oh (Fagaceae), as a surrogate for the disease and to test for changes on the hyphal abundance of ectomycorrhizal fungi. In this study, the flow of phloem to the roots of girdled trees was severed by cutting two narrow incisions (about 10 cm distant) through the inner bark around the circumference of the stem of each tree (fully-girdled), or by cutting two narrow incisions half of the circumference of the tree (half-girdled), to compare with untreated (non-girdled) trees. The hyphal abundance of two common and ecologically important ectomycorrhizal genera (Cenococcum and Tricholoma) was estimated from the roots and surrounding soil using real-time PCR quantification (TaqMan) assay. A significant decrease in the hyphal abundance from soil was observed in girdled tree plots. In contrast, no similar decrease in the root hyphal abundance was observed. Ectomycorrhizal fungi have a major impact on ecosystem function through their control over decomposition, nutrient acquisition, and mobilization and regulation of succession in plant communities. Given their important function, the decline in EM abundance of tanoak infected by P. ramorum will likely disrupt the function and structure of these forests.
Interactive Communication of Balanced Distributions and of Correlated Files

$( X,Y )$ is a pair of random variables distributed over a support set S. Person $P_X $ knows X, person $P_Y $ knows Y, and both know S. Using a predetermined protocol, they exchange binary messages for $P_Y $ to learn X. $P_X$ may or may not learn Y. The m-message complexity $\hat C_m $ is the number of information bits that must be transmitted (by both persons) in, the worst case if only m messages are allowed. $\hat C_\infty $ is the number of bits required when there is no restriction on the number of messages exchanged.A natural class of random pairs is considered. $\hat \mu $ is the maximum number of X values possible with a given Y value. $\hat \eta $ is the maximum number of Y values possible with a given X value. The random pair $( X,Y )$ is balanced if $\hat \mu = \hat \eta $. The following hold for all balanced random pairs. One-way communication requires at most twice the minimum number of bits: $\hat C_1 \leqq 2\hat C_\infty + 1$. This bound is almost tight: For every $\alpha $, there is a ba.
Inner and outer retinal pathways both contribute to surround inhibition of salamander ganglion cells

Illumination of the receptive‐field surround reduces the sensitivity of a retinal ganglion cell to centre illumination. The steady, antagonistic receptive‐field surround of retinal ganglion cells is classically attributed to the signalling of horizontal cells in the outer plexiform layer (OPL). However, amacrine cell signalling in the inner plexiform layer (IPL) also contributes to the steady receptive‐field surround of the ganglion cell. We examined the contributions of these two forms of presynaptic lateral inhibition to ganglion cell light sensitivity by measuring the effects of surround illumination on EPSCs evoked by centre illumination. GABAC receptor antagonists reduced inhibition attributed to dim surround illumination, suggesting that this inhibition was mediated by signalling to bipolar cell axon terminals. Brighter surround illumination further reduced the light sensitivity of the ganglion cell. The bright surround effects on the EPSCs were insensitive to GABA receptor blockers. Perturbing outer retinal signalling with either carbenoxolone or cobalt blocked the effects of the bright surround illumination, but not the effects of dim surround illumination. We found that the light sensitivities of presynaptic, inhibitory pathways in the IPL and OPL were different. GABAC receptor blockers reduced dim surround inhibition, suggesting it was mediated in the IPL. By contrast, carbenoxolone and cobalt reduced bright surround, suggesting it was mediated by horizontal cells in the OPL. Direct amacrine cell input to ganglion cells, mediated by GABAA receptors, comprised another surround pathway that was most effectively activated by bright illumination. Our results suggest that surround activation of lateral pathways in the IPL and OPL differently modulate the sensitivity of the ganglion cell to centre illumination.
The storage and manipulation of radiation dose data in a small digital computer.

Abstract A small dedicated computer has been in routine use for three years for the production of dose distributions for 1,000 patients per year. It has completely replaced hand drawing procedures. Details are given of the physical and computing principles employed in the system. A method of beam tabulation designed to minimize the amount of data stored in the computer and suitable for a wide variety of beams, is described. This method has been found to give accurate results in all parts of filtered or unfiltered beams produced by cobalt 60 and by 6 MeV and 8 MeV linear accelerators. A correction procedure is used which makes accurate compensation for skin curvature and for variations in SSD, which occur in isocentric treatments. The method has been further developed to compensate for tissue inhomogeneities, such as bone and lung, with little reduction in speed of calculation. Finally, methods are described which have been used to obtain beam data in the right form for storage and subsequent retrieval.
Differential amplification of rRNA genes by polymerase chain reaction

The polymerase chain reaction (PCR) is used widely to recover rRNA genes from naturally occurring communities for analysis of population constituents. We have found that this method can result in differential amplification of different rRNA genes. In particular, rDNAs of extremely thermophilic archaebacteria often cannot be amplified by the usual PCR methods. The addition of 5% (wt/vol) acetamide to a PCR mixture containing both archaebacterial and yeast DNA templates minimized nonspecific annealing of the primers and prevented preferential amplification of the yeast small-subunit rRNA genes.
Subclinical atherosclerosis in patients with rheumatoid arthritis

Summary We performed a systematic review with meta-analysis and meta-regression of literature studies evaluating the impact of rheumatoid arthritis (RA) on common carotid artery intima-media thickness (CCAIMT) and on the prevalence of carotid plaques. Studies evaluating the relationship between RA and markers of cardiovascular (CV) risk (CCA-IMT and prevalence of carotid plaques) were systematically searched in the PubMed, Web of Science, Scopus and EMBASE databases. A total of 59 studies (4,317 RA patients and 3,606 controls) were included in the final analysis, 51 studies with data on CCA-IMT (52 data-sets on 3,600 RA patients and 3,020 controls) and 35 studies reporting on the prevalence of carotid plaques (2,859 RA patients and 2,303 controls). As compared to controls, RA patients showed a higher CCA-IMT (mean difference [MD]: 0.10 mm; 95 % confidence interval [CI]: 0.07, 0.12; p < 0.00001), and an increased prevalence of carotid plaques (odds ratio [OR]: 3.61; 95 %CI: 2.65, 4.93; p< 0.00001). Interestingly, when analysing studies on early RA, the difference in CCAIMT among RA patients and controls was even higher (MD: 0.21 mm; 95 %CI: 0.06, 0.35; p=0.006), and difference in the prevalence of carotid plaques was entirely confirmed (OR: 3.57; 95 %CI: 1.69, 7.51; p=0.0008). Meta-regression models showed that male gender and a more severe inflammatory status [as expressed by disease activity score in 28 joints (DAS28), C-reactive protein (CRP) levels, and erythrocyte sedimentation rate (ESR)] significantly impacted on CCA-IMT. In conclusion, RA appears significantly associated with subclinical atherosclerosis and CV risk. These findings can be useful to plan adequate prevention strategies and therapeutic approaches.
Wave Equation Imaging Comparisons: Survey Sinking Vs. Shot Profile Methods

We examine the differences and similarities between the two common categories of wave-equation migration by looking at their mathematical formulations and examining their imaging results. We compare different implementations of shot profile and double square root downward continuation imaging in the context of the overall imaging challenge, including image accuracy, velocity model building, and the ability to generate prestack gathers. We examine the strengths and advantages of the methods by considering the approximations that go into them, the resulting images, and the relative costs of the methods.
Visualization of transmitter release with zinc fluorescence detection at the mouse hippocampal mossy fibre synapse

Exocytosis of synaptic vesicle contents defines the quantal nature of neurotransmitter release. Here we developed a technique to directly assess exocytosis by measuring vesicular zinc release with the zinc‐sensitive dye FluoZin‐3 at the hippocampal mossy fibre (MF) synapse. Using a photodiode, we were able to clearly resolve the zinc fluorescence transient ([Zn2+]t) with a train of five action potentials in mouse hippocampal brain slices. The vesicular origin of [Zn2+]t was verified by the lack of zinc signal in vesicular zinc transporter Znt3‐deficient mice. Manipulating release probability with the application of neuromodulators such as DCG IV, 4‐aminopyridine and forskolin as well as a paired train stimulation protocol altered both the [Zn2+]t and the field excitatory postsynaptic potential (fEPSP) coordinately, strongly indicating that zinc is co‐released with glutamate during exocytosis. Since zinc ions colocalize with glutamate in small clear vesicles and modulate postsynaptic excitability at NMDA and GABA receptors, the findings establish zinc as a cotransmitter during physiological signalling at the mossy fibre synapse. The ability to directly visualize release dynamics with zinc imaging will facilitate the exploration of the molecular pharmacology and plasticity of exocytosis at MF synapses.