Miracle-dz/UniFAR-FTUs huggingface dataset:
ClinGen Cancer Somatic Working Group - Standardizing and democratizing access to cancer molecular diagnostic data to drive translational research

A growing number of academic and community clinics are conducting genomic testing to inform treatment decisions for cancer patients (1). In the last 3-5 years, there has been a rapid increase in clinical use of next generation sequencing (NGS) based cancer molecular diagnostic (MolDx) testing (2). The increasing availability and decreasing cost of tumor genomic profiling means that physicians can now make treatment decisions armed with patient-specific genetic information. Accumulating research in the cancer biology field indicates that there is significant potential to improve cancer patient outcomes by effectively leveraging this rich source of genomic data in treatment planning (3). To achieve truly personalized medicine in oncology, it is critical to catalog cancer sequence variants from MolDx testing for their clinical relevance along with treatment information and patient outcomes, and to do so in a way that supports large-scale data aggregation and new hypothesis generation. One critical challenge to encoding variant data is adopting a standard of annotation of those variants that are clinically actionable. Through the NIH-funded Clinical Genome Resource (ClinGen) (4), in collaboration with NLM's ClinVar database and >50 academic and industry based cancer research organizations, we developed the Minimal Variant Level Data (MVLD) framework to standardize reporting and interpretation of drug associated alterations (5). We are currently involved in collaborative efforts to align the MVLD framework with parallel, complementary sequence variants interpretation clinical guidelines from the Association of Molecular Pathologists (AMP) for clinical labs (6). In order to truly democratize access to MolDx data for care and research needs, these standards must be harmonized to support sharing of clinical cancer variants. Here we describe the processes and methods developed within the ClinGen's Somatic WG in collaboration with over 60 cancer care and research organizations as well as CLIA-certified, CAP-accredited clinical testing labs to develop standards for cancer variant interpretation and sharing.
Interactions between Two Different G Protein-Coupled Receptors in Reproductive Hormone-Producing Cells: The Role of PACAP and Its Receptor PAC1R

Gonadotropin-releasing hormone (GnRH) and gonadotropins are indispensable hormones for maintaining female reproductive functions. In a similar manner to other endocrine hormones, GnRH and gonadotropins are controlled by their principle regulators. Although it has been previously established that GnRH regulates the synthesis and secretion of luteinizing hormone (LH) and follicle-stimulating hormone (FSH)—both gonadotropins—from pituitary gonadotrophs, it has recently become clear that hypothalamic GnRH is under the control of hypothalamic kisspeptin. Prolactin, which is also known as luteotropic hormone and is released from pituitary lactotrophs, stimulates milk production in mammals. Prolactin is also regulated by hypothalamic factors, and it is thought that prolactin synthesis and release are principally under inhibitory control by dopamine through the dopamine D2 receptor. In addition, although it remains unknown whether it is a physiological regulator, thyrotropin-releasing hormone (TRH) is a strong secretagogue for prolactin. Thus, GnRH, LH and FSH, and prolactin are mainly regulated by hypothalamic kisspeptin, GnRH, and TRH, respectively. However, the synthesis and release of these hormones is also modulated by other neuropeptides in the hypothalamus. Pituitary adenylate cyclase-activating polypeptide (PACAP) is a hypothalamic peptide that was first isolated from sheep hypothalamic extracts based on its ability to stimulate cAMP production in anterior pituitary cells. PACAP acts on GnRH neurons and pituitary gonadotrophs and lactotrophs, resulting in the modulation of their hormone producing/secreting functions. Furthermore, the presence of the PACAP type 1 receptor (PAC1R) has been demonstrated in these cells. We have examined how PACAP and PAC1R affect GnRH- and pituitary hormone-secreting cells and interact with their principle regulators. In this review, we describe our understanding of the role of PACAP and PAC1R in the regulation of GnRH neurons, gonadotrophs, and lactotrophs, which are regulated mainly by kisspeptin, GnRH, and TRH, respectively.
Interpreting troponin elevations: do we need multiple diagnoses?

The expanded ability to detect myocardial injury using very sensitive and specific biomarker assays has been a major factor in the evolution of the definition of acute myocardial infarction (MI). This is clearly evident in the ‘Universal Definition of Myocardial Infarction’ recently developed by a joint task force of experts on behalf of the ESC, ACCF, AHA, and WHF (European Society of Cardiology, American College of Cardiology Foundation, American Heart Association, and World Heart Federation). 1 In a clinical setting consistent with myocardial ischaemia, criteria are presented for defining acute MI that include a rise and/or fall in cardiac biomarkers together with symptoms of ischaemia, and/or appropriate ECG changes, and/or imaging evidence of a new regional wall motion abnormality or loss of myocardium. The task force developed a clinical classification of different types of MI that can be briefly summarized as: This multi-component scheme appears to add complexity in an area that can be quite confounding because of the multiple terms used to describe myocardial ischaemia/infarction in all of its various manifestations. This includes differentiating myocardial damage associated with ST elevation (STEMI) from that occurring without ST elevation (non-STEMI). Patients with a sudden change in cardiac status are often admitted to the hospital with a diagnosis of acute coronary syndrome (ACS), but ACS is not included in the ICD-9-CM codes.2 Intermediate coronary syndrome (code 411.1), which includes impending infarction, preinfarction angina, or unstable angina, can be used as a …
Effects of chlorpyrifos and chlorantraniliprole on fermentation quality of alfalfa (Medicago sativa L.) silage inoculated with or without Lactobacillus plantarum LP.

The effects of pesticides and Lactobacillus plantarum (LP) on fermentation quality of alfalfa (Medicago sativa L.) silage were investigated. Chlorpyrifos and chlorantraniliprole were sprayed on the surface of alfalfa plants at 658.6 and 45.0 g active ingredient/ha, respectively. Alfalfa plants were harvested on day 5 post-application and ensiled with or without LP. Chlorpyrifos and chlorantraniliprole decreased the yeast count of alfalfa material (P < 0.05). Both pesticides increased the butyric acid content of alfalfa silage (P < 0.001). Chlorpyrifos increased pH and decreased lactic acid, acetic acid and short-chain fatty acid contents (P < 0.05). LP decreased pH and butyric acid content, and increased lactic acid and short-chain fatty acid contents of alfalfa silage treated with pesticides (P < 0.05). LP increased the concentration of chlorpyrifos residue in alfalfa silage (P < 0.05). Chlorpyrifos and chlorantraniliprole affected the microbial communities of the material before ensiling, especially coliform bacteria and yeast; the two pesticide residues were reduced after the fermentation of alfalfa silage and affected the fermentation process, whereas LP improved the fermentation quality of pesticides-contaminated alfalfa silage and slowed down the dissipation of chlorpyrifos.
Suicide Postvention: Crisis or Opportunity?.

Multiple crises exist within the current tions from experienced members of epidemic of teenage suicide. Although the professional mental health commu prevention is the most direct method nity beyond the school. In this article of saving lives (and is receiving justly we describe the clinical process of deserved attention, e.g., Farberow, school-based postvention (as devel Atman, & Thorne, 1985), suicides do oped by Youth Suicide Prevention Ser continue to occur among children, advices [YSPS] in the Department of Psy olescents, and young adults; these chiatry at Albert Einstein Medical deaths pose difficult challenges requirCenter, Philadelphia) in order to share ing complex responses. Beyond the iniour experience with other colleagues tial tragedy of a young life lost, suicide and encourage further use of this in creates "survivors," with groups of tervention. youngsters left behind to suffer Although postvention activities are through the shock and bereavement. best organized in advance of any actual Although the increased risk of suicidal emergency (Lamb & Dunne-Maxim, activity associated with suicide survi1987), necessity frequently requires vorship is most severe with immediate rapid enactment of previously vague family and friends, this risk (Smith & plans. In the latter cases, concern about Crawford, 1986; Mcintosh, 1987) excontagion can hinder acceptance of tends throughout the community of postvention, whereas prior knowledge the deceased, having substantial impact provides a cushion against the shock of at the youngster's school. Fortunately, suicideNevertheless, most postvention this frightening situation can be adprograms begin after the fact, as did dressed through postvention (Shneidour own' °ur current procedure is to man, 1971; 1975), which provides asoffer P°stvention services to school ad sistance to the survivors of a suicide. mimstrators and faculty members as
MapMyFlu: visualizing spatio-temporal relationships between related influenza sequences

Understanding the molecular dynamics of viral spreading is crucial for anticipating the epidemiological implications of disease outbreaks. In the case of influenza, reassortments or point mutations affect the adaption to new hosts or resistance to anti-viral drugs and can determine whether a new strain will result in a pandemic infection or a less severe progression. To this end, tools integrating molecular information with epidemiological parameters are important to understand how molecular characteristics reflect in the infection dynamics. We present a new web tool, MapMyFlu, which allows to spatially and temporally display influenza viruses related to a query sequence on a Google Map based on BLAST results against the NCBI Influenza Database. Temporal and geographical trends appear clearly and may help in reconstructing the evolutionary history of a particular sequence. The tool is accessible through a web server, hence without the need for local installation. The website has an intuitive design and provides an easy-to-use service, and is available at http://mapmyflu.ipmb. uni-heidelberg.de
Microbial Degradation of Lobster Shells to Extract Chitin Derivatives for Plant Disease Management

Biodegradation of lobster shells by chitinolytic microorganisms are an environment safe approach to utilize lobster processing wastes for chitin derivation. In this study, we report degradation activities of two microbes, “S223” and “S224” isolated from soil samples that had the highest rate of deproteinization, demineralization and chitinolysis among ten microorganisms screened. Isolates S223 and S224 had 27.3 and 103.8 protease units mg-1 protein and 12.3 and 11.2 μg ml-1 of calcium in their samples, respectively, after 1 week of incubation with raw lobster shells. Further, S223 contained 23.8 μg ml-1 of N-Acetylglucosamine on day 3, while S224 had 27.3 μg ml-1 on day 7 of incubation with chitin. Morphological observations and 16S rDNA sequencing suggested both the isolates were Streptomyces. The culture conditions were optimized for efficient degradation of lobster shells and chitinase (∼30 kDa) was purified from crude extract by affinity chromatography. The digested lobster shell extracts induced disease resistance in Arabidopsis by induction of defense related genes (PR1 > 500-fold, PDF1.2 > 40-fold) upon Pseudomonas syringae and Botrytis cinerea infection. The study suggests that soil microbes aid in sustainable bioconversion of lobster shells and extraction of chitin derivatives that could be applied in plant protection.
Privacy-preserving Twitter-based solution for visually impaired people

Visually impaired people is a big community all over the world. They usually seek help to perform their daily activities such as reading the expired date of food cans or medicine, reading out PIN of a certain ATM Visa, identifying the color of clothes or differentiate between the money notes and other objects with the same shape. A number of IT-based solutions have been proposed to help and assist blind and/or visually impaired people. Generally speaking, these solutions, however, do not support Arabic languages nor protect blind users’ privacy. In this paper, Trusted Blind Society (TBS) mobile application is proposed. It is an android application which allows blind users to recognize their unknown surroundings by utilizing two concepts: social networks sites and friendsourcing. These two concepts were employed by allowing family members and the trusted friends, who are registered on Twitter, to answer blind users’ questions on a real time. The solution is also bilingual, supports (Arabic/English) and allows screen reader using Android talk-back service. The performance of the TBS system was evaluated using loader.io to check its stability under the heavy load and it was tested by a number of blind volunteers and the results showed good performance comparing to most related work.
Optimized memory access support for data layout conversion on heterogeneous multi-core systems

Heterogeneous multi-core systems that contain multiple CPUs and GPUs are gaining momentum, as they are providing different computation power to meet the performance demand of modern applications. On such systems, developers try to fully utilize the computation power both for CPU and GPU by using the emerging programming models such as CUDA and OpenCL. To achieve the maximal performance, developers must carefully offload the appropriate workload to the compute devices according to the characteristics of target architecture. Under such scenario, seamlessly data motion between different processors become crucial. Additionally, re-organizing the data layout to fit the target architectures, such as array-of-structure (AOS) for CPU, structure-of-array (SOA) for GPU, and coordinate (COO) format to ELLPACK (ELL) for sparse computation, address such concern. In this paper, we propose a hardware memory manager, which efficiently optimizes the conversion of data layouts for heterogeneous multi-core systems on-the-fly. We address coalescing and sparse format conversion issue in our design. A novel ping-pong transpose architecture is devised to reorganize non-coalescing access pattern, and a histogram unit and sparse address generator are presented to process sparse storage format transformation. Our design reduces the overhead of data transfer and layout transformation among CPU and GPU. In our experiment, our design achieves 68.5 to 2.19 times speed up comparing to software-based library depending on data size.
Analysis of Traveling-Wave-Fed Patch Arrays

The design and analysis of traveling-wave-fed, circularly polarized, concentric ring arrays are presented. Linearly polarized microstrip radiating elements were used in the arrays, and fed in series by non-radiating apertures. High quality circular polarization (CP) was achieved by arranging the radiating patches in a concentric ring, with the patches fed with currents of the same magnitude and the appropriate phase delays. For the first time in the literature, a full-wave based model of the power distribution to each element is presented. This model formed the basis of a rigorous analysis of the antenna, not addressed by previous authors. Such analysis is essential to ensure that all the elements radiate identical amount of power, and thus maintain pattern symmetry and optimum CP characteristics. The proposed designs were validated through practical measurements, which showed good CP quality and well-defined radiation patterns.
Mesh routing for IPv 6 over 802 . 15 . 4 on TinyOS

Wireless Sensor Networks are made up of autonomous devices which carry different sensors with the aim of monitoring their environment. These motes are usually very low-power consuming devices and provide limited processing capabilities. A special purpose Operating System, TinyOS, is frequently used on them. Motes generally form ad-hoc networks in order to exchange information from their sensors and collect it at a more capable computing device. TinyOS relies on Active Messages for this task. However, an IPv6 stack, based on the 6lowpan specification, has been implemented so that applications running on the system can use IP and higher level protocols that use IP for transport in their communication. A missing piece of the implementation is a mesh routing component that will allow messages to travel through intermediate nodes. Two such components have also been developed, based on the LOAD and DYMO-low routing protocols, but they work independently of the IPv6 stack. This project aims to integrate them into the 6lowpan implementation so that it makes use of their functionality. The goal is for this to be transparent to application code that already uses IPv6. This report describes the integration strategy goals and design, discusses problems encountered during the work and identifies several areas for further improvement and research.
Identification and characterization of methicillin-resistant coagulase-negative staphylococci from bovine mastitis.

OBJECTIVES This study focused on the correlation between geno- and phenotypic tests in the correct assessment of mecA-mediated methicillin resistance among coagulase-negative staphylococci (CoNS) and the further characterization of mecA-positive isolates. METHODS A total of 121 CoNS from cases of bovine mastitis were investigated for oxacillin susceptibility by disc diffusion and broth microdilution. Isolates classified as methicillin resistant by either method were tested by PCR for the mecA gene and the SCCmec type. The cefoxitin disc test was also applied. PFGE served to determine the genetic relationships of the resistant isolates. RESULTS Sixteen isolates were classified as methicillin resistant and 96 isolates as methicillin susceptible by both methods. The mecA gene was identified in 15 of the 16 resistant isolates. Nine mecA-negative isolates showed oxacillin MICs of 0.5 or 1 mg/L, oxacillin zone sizes of 18-23 mm and were classified as methicillin susceptible in the cefoxitin disc test. SCCmec cassettes of types V (five Staphylococcus haemolyticus), III (one Staphylococcus saprophyticus), IV (five Staphylococcus epidermidis, one Staphylococcus capitis) and IV with an additional ccrA4/B4 gene (two S. epidermidis) were seen, while one S. epidermidis carried a non-typeable SCCmec element (mec complex B + no ccr gene complex detected). All isolates with SCCmec type IV or non-typeable cassettes exhibited low oxacillin MICs of 1-4 mg/L, whereas isolates with type III or V cassettes had MICs of >or=16 mg/L. CONCLUSIONS CoNS with oxacillin MICs of 0.5 and 1 mg/L should be confirmed for the presence of mecA before reporting them as methicillin resistant.
Reduced nitric oxide synthase activity in rats with chronic renal disease due to glomerulonephritis.

BACKGROUND Animal studies with systemic nitric oxide synthase (NOS) inhibition and renal ablation, suggest that NO deficiency is both a cause and a consequence of chronic renal disease (CRD). METHODS This study examined a glomerulonephritis (GN) model of CRD to determine if NO is deficient. In addition to measuring indices of renal function (proteinuria, creatinine clearance, structural damage), indices of total and renal nitric oxide production also were assessed (total NO(X) excretion, renal NOS activity, renal NOS protein abundance, plasma levels of NOS substrate and endogenous inhibitor). RESULTS Rats developed increasing proteinuria 12 to 20 weeks after induction of GN (with anti-glomerular basement membrane, GBM, antibody) and at 20 weeks exhibited reduced creatinine clearances and increased glomerulosclerosis relative to age-matched controls. Total NO(X) excretion was reduced and the renal cortical NOS activity and neuronal NOS (nNOS) abundance was decreased relative to controls. There was no impact on renal or aortic endothelial NOS expression or cerebellar nNOS. The plasma l-arginine (Arg) concentration was well maintained but plasma asymmetric dimethylarginine (ADMA) concentration increased in GN versus control animals. CONCLUSIONS Total and renal NOS activity is reduced in the GN model of CRD due to increased circulating endogenous NOS inhibitors and decreased renal nNOS abundance.
MobileSSI - A Multi-modal Framework for Social Signal Interpretation on Mobile Devices

Over the last years, new generations of mobile devices have found their way into our pockets. They provide more and more computational power and memory capacity to perform complex calculations that formerly could only be accomplished with bulky desktop machines. Moreover, mobile devices are equipped with a range of sensors to capture people's motion, environmental sound etc. These capabilities combined with the willingness of people to permanently carry them around open up completely new ways of observing human behaviour no longer in laboratories, but "in the wild". However, the detection and analysis of social cues is still a challenging task and requires adequate tools to synchronise, process and analyse relevant signals. This may be the reason why many studies and applications focus on offline analysis and typically collect data over long periods of time and analyse them afterwards. To allow for immediate feedback, real-time assessment is necessary. In this paper, we present MobileSSI, a port of the Social Signal Interpretation (SSI) framework to Android and embedded Linux platforms. The framework supports the joint development of processing pipelines for the analysis of social signals on a desktop computer and mobile devices. Throughout the paper we report on challenges we had to face when porting SSI to a mobile context. Furthermore, we summarise first experiences with a real-life setting in a pub where we focused on the analysis of multimodal social group dynamics investigating laughter as a sign of enjoyment.
Acquisition of Practical Knowledge by Blind and Visually Impaired Students in Grades 8–12

The Test of Practical Knowledge was used to measure the acquisition of practical knowledge in 116 blind and visually impaired adolescents in public and residential schools in Texas. Most of the demographic variables were found to have little or no relationship to acquired practical knowledge. Furthermore, although students from both types of schools performed poorly compared to sighted norms, it was found that legally blind–visually impaired students had more difficulty in acquiring practical knowledge than did their totally blind peers.