Miracle-dz/UniFAR-FTUs huggingface dataset:
Defining and managing incidental findings in genetic and genomic practice

The rapidly declining costs and increasing speeds of whole-genome analysis mean that genetic testing is undergoing a shift from targeted approaches to broader ones that look at the entire genome. As whole-genome technologies gain widespread use, questions about the management of so-called incidental findings—those unrelated to the question being asked—need urgent consideration. In this review, we bring together current understanding and arguments about (1) appropriate terminology, (2) the determination of clinical utility and when to disclose incidental findings, (3) the differences in management and disclosure in clinical, research and commercial contexts and (4) ethical and practical issues about familial implications and recontacting those tested. We recommend that greater international consensus is developed around the disclosure and management of incidental findings, with particular attention to when, and how, less clear-cut results should be communicated. We suggest that there is no single term that captures all the issues around these kinds of findings and that different terms may, therefore, need to be used in different settings. We also encourage the use of clear consent processes, but suggest that the absence of consent should not always preclude disclosure. Finally, we recommend further research to identify ways to implement the use of a genome output as a resource, accessible over time, to facilitate appropriate disclosure and recontact when the significance of a previously unclear incidental finding is clarified.
Synchronization of coupled dynamic systems using fuzzy design approach

This paper proposes a brand new T-S fuzzy model-based approach to achieve synchronization of coupled dynamical systems. The T-S fuzzy models are given to exactly represent the coupled dynamical systems. Then the model-based fuzzy synchronization design is carried out for each subsystem utilizing the concept of parallel distributed compensation(PDC). We analyze the stability of the overall fuzzy synchronization system by applying Lyapunov stability theory and derive stability conditions by solving linear matrix inequalities (LMI) problem. The methodology proposed here can be applied to continuous-time and discrete-time dynamic systems. A well known example, the driven pendulum model is used for the demonstration. It is noted that the coupled pendulum system can be regarded as an important engineering application. Indeed it can simply represent a model of a robot arm or a robot foot. Several numerical simulations for the synchronization of coupled dynamical system illustrate the effectiveness of the proposed scheme.
Air Quality Assessment using Neural Networks and Fuzzy Logic

Traditional air quality assessment is realized using air quality indices which are determined as mean values of selected air pollutants. Thus, air quality assessment depends on strictly given limits without taking into account specific local conditions and synergic relations between air pollutants and other meteorological factors. The stated limitations can be eliminated, e.g. using systems based on neural networks and fuzzy logic. Therefore, the paper presents a design of a model for air quality assessment based on a combination of Kohonen’s self-organizing feature maps and fuzzy logic neural networks. The model makes it possible to analyze the structure of data, to find localities with similar air quality and to interpret the classification results by means of fuzzy logic. Due to its generalization ability, it is also possible to classify unknown localities into classes assessing their air quality. Key-Words: Air quality, assessment, neural networks, fuzzy logic, neuro-fuzzy systems.
Association of diabetes mellitus with use of atypical neuroleptics in the treatment of schizophrenia.

OBJECTIVE The development of both type I and type II diabetes after initiation of some atypical neuroleptics has been reported, primarily in studies involving small series of patients. This study used administrative data from a large national sample of patients with a diagnosis of schizophrenia to compare the prevalence of diabetes mellitus in patients receiving prescriptions for atypical and typical neuroleptics. METHOD All outpatients with schizophrenia treated with typical and atypical neuroleptics over 4 months in 1999 in the Veterans Health Administration of the Department of Veterans Affairs (VA) were included in this study. Patients treated with atypical neuroleptics were those who received prescriptions for clozapine, olanzapine, risperidone, or quetiapine. Patients with a diagnosis of diabetes were also identified by using ICD-9 codes in VA administrative databases. The prevalence of diabetes mellitus across age groups and among patients receiving prescriptions for different atypical neuroleptics was examined with multiple logistic regression. RESULTS A total of 38,632 patients were included in the study: 15,984 (41.4%) received typical neuroleptics and 22,648 (58.6%) received any atypical neuroleptic (1,207 [5.3%] received clozapine; 10,970 [48.4%], olanzapine; 955 [4.2%], quetiapine; and 9,903 [43.7%], risperidone; 387 patients received prescriptions for more than one atypical neuroleptic). When the effects of age were controlled, patients who received atypical neuroleptics were 9% more likely to have diabetes than those who received typical neuroleptics, and the prevalence of diabetes was significantly increased for patients who received clozapine, olanzapine, and quetiapine, but not risperidone. However, for patients less than 40 years old, all of the atypical neuroleptics were associated with a significantly increased prevalence of diabetes. CONCLUSIONS In this large group of patients with schizophrenia, receipt of a prescription for atypical neuroleptics was significantly associated with diabetes mellitus.
Longitudinal Tethering of Arteries in Dogs

The magnitude and properties of longitudinal vascular tethering were studied in the thoracic aorta, abdominal aorta, and femoral artery of 23 dogs. The tethering was found to consist of a dominant viscoelastic restraining element that demonstrated a moderate degree of stress relaxation and a significant inertial component that was related to the mass of the vessel and its surrounding tissues (the “added mass”). Static and dynamic studies of these properties showed them to be surprisingly linear. The simplest linear model that could simulate these experimental data consisted of two elastic components, two frictional components and a lumped inertial component. Within the physiologic range of frequencies (1 to 20 cycles/sec), the two elastic components became dynamically coupled so that they appeared to act as a single spring, the stiffness of which could be characterized by a “dynamic spring constant. ” The mean value of the dynamic spring constant was 12 g/cm3 for the thoracic aorta; it increased along the aorta toward the femoral artery to almost 70 times that value. Contrary to the simple tethering model assumed by Womersley, these data showed that the mechanical behavior of the system is strongly influenced by frictional components.
Méthodes de simulations rapides du lien radio pour les systèmes 3G

Les simulations du lien radio des systemes a etalement de spectre de troisieme generation sont tres lentes a executer a cause de la complexite des traitements realises. Cette complexite provient principalement de la simulation de la correlation temporelle du canal multi-trajets et du recepteur en râteau qui fonctionne avec plusieurs echantillons par chip. Dans ce travail de these nous proposons principalement trois approches pour accelerer le temps de simulations: - La premiere consiste a exploiter la propriete de bande limitee du spectre Doppler du canal et a generer le canal par une chaine de Markov de premier ordre suivie d'une interpolation. - La deuxieme consiste a remarquer le fait que le spectre de l'energie utile a la sortie du recepteur en râteau est aussi a bande limitee et a generer directement la sortie du recepteur par une chaine de Markov d'ordre variable suivie d'une interpolation. - Lorsque les retards du canal ne sont pas des multiples de la duree d'un chip, le recepteur fonctionne avec plusieurs echantillons par chip permettant ainsi d'evaluer correctement les performances du systeme. La troisieme approche consiste a trouver un canal multi-trajets equivalent au canal reel mais ayant des retards mutuellement independants et multiples de la duree d'un chip. Ceci permet d'eviter la simulation des filtres d'emission et de reception. Ces approches peuvent etre combinees afin d'avoir des outils rapides de simulation du lien radio. Un autre aspect traite dans cette these est l'etude de l'effet de l'estimation usuelle du canal a partir des symboles pilotes sur les performances du systeme. Cette estimation a un impact important sur la boucle de controle de puissance pour les canaux ayant des retards inferieurs a la duree d'un chip.
Estimación de Parámetros Cinéticos de la Degradación Aeróbica de Efluentes Lácteos usando AQUASIM v 2.1b

Resumen Se estimaron parametros cineticos del mecanismo de biodegradacion aerobica de efluentes lacteos, empleando tecnicas de simulacion, estimacion de parametros y analisis sensitivo, disponibles en el software Aquasim v 2.1b. Se utilizo un reactor tanque agitado discontinuo de 4 litros de capacidad con inyeccion de aire permanente. El consumo de sustrato se represento considerando cinetica de primer orden en un caso y del tipo de Monod en el otro. Se obtuvo un elevado valor de la constante de Monod, K S , lo cual limito el analisis a la primera alternativa. Los valores hallados de los parametros de respiracion endogena k d y sintesis celular Y, fueron similares en ambos casos, mientras que el analisis sensitivo determino parametros de Monod no identificables. Se concluye que para este caso resulta valida una cinetica de primer orden para representar el consumo de sustrato y se destaca la importancia de esta herramienta para efectuar el analisis. Palabras claves: efluentes lacteos, biodegradacion, parametros cineticos, analisis de sensitividad
Rapid and reversible disappearance of beta‐adrenergic cell surface receptors.

The water soluble beta‐adrenergic ligand [3H]CGP‐12177 was used to measure the cell surface receptors in intact cells. In two cell lines, C6 glioma and WEHI 7 lymphoma cells, ‐50% of the cell surface receptors disappear within minutes of incubation of the cells with isoproterenol. The receptors can still be detected in homogenates and reappear on the cell surface when cells are washed and reincubated at 37 degrees C. The data agree with a disappearance of the receptors from the cell surface by an agonist‐mediated endocytosis.
Cefazolin versus Nafcillin for Methicillin-Sensitive Staphylococcus aureus Bloodstream Infection in a California Tertiary Medical Center

ABSTRACT Recent observational studies have suggested possible reductions in mortality in patients receiving cefazolin versus antistaphylococcal penicillins. We examined 90-day mortality in patients receiving cefazolin compared to nafcillin for methicillin-susceptible Staphylococcus aureus (MSSA) bloodstream infection (BSI). We identified persons with MSSA BSI admitted to San Francisco General Hospital from January 2008 to July 2013 through a hospital-wide infection surveillance system and confirmed 90-day mortality using U.S. national vital registries. We included persons receiving cefazolin or nafcillin as the predominant intravenous antimicrobial agent; all participants received inpatient Infectious Diseases service consultation. We estimated the association between receipt of cefazolin and 90-day risk of death by multivariate logistic regression, including a propensity score for receiving cefazolin as the second predictor. Of 230 MSSA BSI cases, 30 received nafcillin and 70 received cefazolin as the predominant antimicrobial; 10 died within 90 days, 5 from each group. Unadjusted analysis showed substantial but not statistically significant reduced odds of death in those receiving cefazolin (odds ratio, 0.38; 95% confidence interval [CI], 0.10 to 1.44). Multivariate analysis with propensity scores found a similar adjusted odds ratio (0.40; 95% CI, 0.09 to 1.74; P = 0.22). We found a large reduction in 90-day mortality in those receiving cefazolin compared to nafcillin for MSSA BSI, but this finding was not statistically significant. The magnitude of effect seen in this and other studies justifies further study.
Residues Throughout the Cytoplasmic Domain Affect the Internalization Efficiency of P-selectin (*)

The cytoplasmic domains of many membrane proteins have short sequences, usually including a tyrosine or a di-leucine, that function as sorting signals. P-selectin is an adhesion receptor for leukocytes that is expressed on activated platelets and endothelial cells. Its 35-residue cytoplasmic domain contains signals for sorting into regulated secretory granules, for endocytosis, and for movement from endosomes to lysosomes. The domain has a membrane-distal sequence, YGVFTNAAF, that resembles some tyrosine-based signals. We studied the effects of deletions and mutations in the cytoplasmic tail of human P-selectin on its internalization in clathrin-coated pits of transfected Chinese hamster ovary cells. Mutations and deletions in the putative tyrosine-based motif did not clearly implicate these residues as critical components of a short internalization signal. Indeed, a construct containing a truncated 18-residue cytoplasmic domain with a single substitution (K761A/H773Stop) was internalized nearly three times as fast as wild-type P-selectin; this construct contained no di-leucine, tyrosine, or other known sorting motif. Substitution of residues throughout the cytoplasmic domain affected the internalization rate of P-selectin. Furthermore, the cytoplasmic domain of P-selectin mediated faster internalization when attached to the extracellular and transmembrane domains of the low density lipoprotein receptor than when attached to the corresponding domains of P-selectin. Thus, we were unable to identify a short internalization signal in the cytoplasmic tail of P-selectin. Residues throughout the cytoplasmic domain, and perhaps the transmembrane sequence to which the domain is attached, affect the efficiency of internalization.
Multi-scale non-local means with shape prior for enhancement of cell membrane images

Light sheet microscopy allows rapid optical sectioning of whole chicken embryos during early development, visualizing cells through transgenic expression of a fluorescent cell membrane label. Low signal-to-noise ratios and large variability in intensity make segmentation of these images difficult, often resulting in discontinuous cell edges. We propose a multi-scale non-local means with shape prior (MS-NLM-SP) method for image enhancement, which takes into account cell-specific characteristics, such as size, geometry, and periodicity. Investigating theoretical connections between our approach and anisotropic diffusion reveals that the first step, detail-enhanced multi-scale representation, corresponds to selective backward diffusion, while the second step of MS-NLM-SP resembles anisotropic forward diffusion. Experimental results show that incorporating cell-specific features into non-local image denoising methods improves subsequent segmentation.
Analysis of killer cell immunoglobulin-like receptors and their human leukocyte antigen-ligands gene polymorphisms in Iranian patients with systemic lupus erythematosus

Objective Systemic lupus erythematosus (SLE) is an inflammatory autoimmune disease. Natural killer (NK) cells play a critical role in the pathogenesis of autoimmune disorders that mainly express killer cell immunoglobulin-like receptors (KIRs). The present study was undertaken to determine the association of the KIR alleles, genotypes, and KIR–human leukocyte antigen (HLA) ligand gene combinations with the susceptibility to SLE. Methods The genotyping of 17 KIR and 5 HLA loci was performed using the polymerase chain reaction-sequence specific primer (PCR-SSP) method. The study population consisted of 230 SLE patients and 273 ethnical-, age-, and sex-matched healthy controls. The association of the polymorphisms with the prevalence of 11 clinical criteria in patients was analyzed. Results The carrier frequency of HLA-A-Bw4 was modestly decreased in the SLE patients. The prevalence of hematological and renal disorders was significantly increased in patients with combination of KIR3DL1+; HLA-B-Bw4Thr80+ and KIR2DS1+; HLA-C2+ genes, respectively. Female patients with combination of KIR2DL2+; HLA-C1− genes were more likely to develop serositis. In addition the prevalence of renal disorders, oral ulcer and serositis was significantly increased in male patients with KIR3DP1+, KIR2DS1+, and KIR2DS3+ genotypes respectively. Conclusion Our results showed that the presence of activating KIR receptors alone or in combination with their HLA ligands and the absence of inhibitory KIRs in combination with their HLA ligands may activate NK cells and are significantly correlated with the prevalence of renal disease, hematologic disorders, serositis, and oral ulcer in SLE patients.
Glycosylation of herpes simplex virus type 1 gC in the presence of tunicamycin

The presence of O-glycosidic linkages on herpes simplex virus type 1 (HSV-1) glycoproteins was indicated by the synthesis and glycosylation of HSV-1 glycoproteins in the presence of tunicamycin. Monospecific antiserum to HSV-1 gC immunoprecipitated a 92,000-molecular-weight protein synthesized in the presence of tunicamycin and isotopically labeled with glucosamine or galactose. Anti-gAB did not immunoprecipitate a carbohydrate-labeled HSV-1 protein synthesized in the presence of tunicamycin. The purified glucosamine-labeled 92,000-molecular-weight protein synthesized in the presence of tunicamycin and the fully glycosylated forms of gAB and gC were tested for their sensitivity to mild alkaline hydrolysis. Purified gAB was resistant to mild alkaline hydrolysis, whereas gC and the 92,000-molecular-weight protein were both sensitive to mild alkaline hydrolysis. These results suggest that O-glycosidic linkages are associated with the HSV-1 gC glycoprotein.
Le langage est-il un instinct ? Une critique du nativisme linguistique, de Chomsky à Pinker

SOMMAIRE Introduction A. Avant Pinker, Chomsky A.2 Le langage comme instinct et système A.3 Le langage libéré de la communication A.4 Le langage comme compétence: la Grammaire Universelle A.6 Composants du “génotype” B. Chomsky : Arguments en faveur de l'innéité B.1 Arguments non linguistiques B.2 Arguments linguistiques B.2. 1 Arguments linguistiques en faveur de l'innéité 1: impuissance des procédures empiristes B.2. 2 Arguments linguistiques en faveur de l'innéité 2: insuffisance des DLP C. Portée idéologique du nativisme D. Après Chomsky : la question de l’acquisition D.1 Arguments nativistes sur l’acquisition du langage D.2 L’argument de la sélectivité D.3 L’argument de la sous-exposition D.3. 1 L’argument des cultures taciturnes D.3. 2 L’argument de la sous-exposition (suite) : la créolisation D.3. 3 L’argument de la sous-exposition (suite) : les enfants sourds D.3. 4 L’argument de la sous-exposition (suite) : la langue des signes nicaraguayenne D.3. 5 L’argument de la sous-exposition (suite) : le cas Simon
Chromosome micro‐dissection and region‐specific libraries from pachytene chromosomes of maize (Zea mays L.)

Summary For the first time, pachytene chromosomes have been used for micro-dissection, amplification and cloning using the short arm of maize chromosome 6. For this purpose, methods for the preparation of unstained pachytene chromosomes were developed. In two separate experiments, 10 and 12 segments of the satellite region were isolated utilizing glass needles and DNA was amplified by linker-adaptor-PCR. After amplification, maize-specific DNA was verified by genomic Southern hybridizations. Chromosomal in situ suppression hybridization confirmed that the adaptor PCR products originated from the micro-dissected 6S region. The adaptor PCR products were cloned into a plasmid vector and the chromosome region-specific libraries were characterized.
A Genome Segment on Mouse Chromosome 12 Determines Maxillary Growth

The primary and modifier genes that regulate normal maxillofacial development are unknown. Previous quantitative trait locus (QTL) analyses using the F2 progeny of 2 mouse strains, DBA/2J (short snout/wide face) and C57BL/6J (long snout/narrow face), revealed a significant logarithm-of-odds (LOD) score for snout length on mouse chromosome 12 at 44 centimorgan (cM). We further sought to validate this locus contributing to anterior-posterior dimensions of the upper mid-face at the D12Mit7 marker in a 44-centimorgan portion of chromosome 12. Congenic mice carrying introgressed DNA from DBA/2J on a C57BL/6J background were selected for submental vertex cephalometric imaging. Results confirmed QTLs, determining that short snout length (P < 0.05) and face width relative to snout length (P < 0.01) were present in the 44-cM region of chromosome 12. We conclude that one or more genes contributing to the shape of the maxillary complex are located near 44 cM of mouse chromosome 12.
Sonographic approach to diagnosing pulmonary consolidation

Thirty‐nine consecutive patients with consolidated lung confirmed radiologically underwent sonography, and their sonograms were compared with results for 100 healthy subjects. The hyperechoic line of normal aerated lung and its air artifacts showed respiratory motions ("gliding sign," n = 100). Patients with pneumonia demonstrated distinct sonographic patterns. Strong linear echoes with characteristic air artifacts (air bronchogram) and anechoic tubular structures (fluid bronchogram) were visualized in 36 of 39 patients (92.30%). The superficial lung showed a homogeneous hypoechoic band termed "superficial fluid alveolograms" (n = 39) with respiratory motions in 35 of 39 patients. We conclude that sonography can evaluate pulmonary consolidation and may provide additional roentgenographic information, especially when fluid bronchograms are visualized.
Asynchronous Time encoder based quasi-Static modelling for Human Area Network in VANET

Power constraints play a key role in designing Huma n Area Networks (HANs) for bio authentication vehicle based on driver’s identity. To alleviate th e power constraints, we advocate a design that uses an asynchronous time encoding mechanisms for representing bio authentication information and the skin surface as the communication channel. Time encoding does not require a clock while allows perfect sign al recovery; the communication channel is operated bel ow 1 MHz We (i) review the fundamental theory behind time encoding and signal recovery, (ii) desc ribe the implementation of a HAN prototype, (iii) describes the implementation of bio authentication for vehicle identity and (iv) present research data obtained from our experimental platform. We demonstrate that the fidelity of the proposed signal representation and transmission scheme is well abov e the bio medical monitoring requirements even in t he case of additive channel-noise and neighbouring cha nnel interference. Consequently, the traditional HA N architecture consisting of clocked A/D converters f eeding into digital RF channels can be replaced wit h a less power demanding time encoding/decoding pair that uses the skin surface as a communications channe l. Here we propose a multilayer mathematical model using volume conductor theory for galvanic coupling HAN on a human limb with consideration on the inhomogeneous properties of human tissue. By introducing and checking with quasi-static approxim ation criteria, Maxwell’s equations are decoupled a nd capacitance effect is included to the governing equ ation for further improvement. Finally, the accurac y and potential of the model are examined.