Miracle-dz/UniFAR-FTUs huggingface dataset:
Epigenotype-phenotype correlations in Beckwith-Wiedemann syndrome

Beckwith-Wiedemann syndrome (BWS) is a model imprinting disorder resulting from mutations or epigenetic events involving imprinted genes at chromosome 11p15.5. Thus, germline mutations inCDKN1C, uniparental disomy (UPD), and loss of imprinting of IGF2 and other imprinted genes have been implicated. Many familial BWS cases have germlineCDKN1C mutations. However, most BWS cases are sporadic and UPD or putative imprinting errors predominate in this group. We have identified previously a subgroup of sporadic cases with loss of imprinting (LOI) of IGF2 and epigenetic silencing of H19 proposed to be caused by a defect in a distal 11p15.5 imprinting control element (designated BWSIC1). However, many sporadic BWS patients show biallelicIGF2 expression in the presence of normalH19 methylation and expression patterns. This and other evidence suggested the existence of a further imprinting control element (BWSIC2) at 11p15.5. Recently, we showed that a subgroup of BWS patients have loss of methylation (LOM) at a differentially methylated region (KvDMR1) within theKCNQ1 gene centromeric to theIGF2 and H19genes. We have now analysed a large series of sporadic cases to define the frequency and phenotypic correlates of epigenetic abnormalities in BWS. LOM at KvDMR1 was detected by Southern analysis or a novel PCR based method in 35 of 69 (51%) sporadic BWS without UPD. LOM at KvDMR1 was often, but not invariably associated with LOI ofIGF2. KvDMR1 LOM was not detected in BWS patients with putative BWSIC1 defects and cases with KvDMR1 LOM (that is, putative BWSIC2 defects) invariably had a normalH19 methylation pattern. The incidence of exomphalos in putative BWSIC2 defect patients was not significantly different from that in patients with germlineCDKN1C mutations (20/29 and 13/15 respectively), but was significantly greater than that in patients with putative BWSIC1 defects (0/5, p=0.007) and UPD (0/22, p<0.0001). These findings are consistent with the hypothesis that LOM of KvDMR1 (BWSIC2 defect) results in epigenetic silencing ofCDKN1C and variable LOI ofIGF2. BWS patients with embryonal tumours have UPD or a BWSIC1 defect but not LOM of KvDMR1. This study has further shown how (1) variations in phenotypic expression of BWS may be linked to specific molecular subgroups and (2) molecular analysis of BWS can provide insights into mechanisms of imprinting regulation.
Gastric Carcinoma With Lymphoid Stroma: Incidence of EBV and Helicobacter pylori Infection

Lymphoepithelioma-like carcinoma (LELC) of the stomach is reported to be associated with Epstein-Barr virus (EBV) and to have a better prognosis than typical adenocarcinoma. However, the incidence of EBV and its association with Helicobacter pylori is controversial. In our series, 9 of 370 (2.4%) cases of gastric adenocarcinoma were LELC. Formalin-fixed, paraffin-embedded LELC tissue was immunostained with monoclonal antibodies against CD3, CD20, and Ki-67. Warthin–Starry stain for H. pylori and in situ hybridization for EBV were performed. As a control, 21 cases of adenocarcinoma with prominent lymphoid stroma were compared with LELC. The most common location of LELC was the body of the stomach (five cases), followed by the cardia (two cases), whereas the antrum was the most common site for the control group. There were no significant differences in age, sex, or lymph node metastasis between the LELC and control groups. The mean Ki-67 index was similar (38.2% in LELC versus 35.3% in control). H. pylori was found in 2 LELC cases (22%) and 6 controls (28.5%). EBV was positive in 7 LELC cases (77.8%) and 4 controls (19.0%). All patients with LELC are alive and well, whereas three patients have died of their disease in the control group. Although EBV appeared to be a contributing factor, H. pylori had a minor role in LELC. There were no clinicopathologic differences between LELC and the control group, except for the location of the tumor in the body of the stomach and the tendency toward a better prognosis in LELC.
An improved Poisson Surface Reconstruction algorithm

In this paper we describe an improved Poisson Surface Reconstruction algorithm. The Poisson Surface Reconstruction method considers all the points at once, without resorting to heuristic spatial partitioning or blending, and use the Marching Cubes algorithm to get the representations. We introduce an improved Marching Cubes algorithm to Poisson Surface Reconstruction method to generate more realizing representations. The improved MC algorithm includes interpolating between data points and fast searching based on data segmentation. Experimenting with publicly available scan data, we demonstrate reconstruction of surface with greater detail and more efficiency.
Praxisstudie ambulante Psychotherapie Schweiz (PAP-S): Studiendesign und Machbarkeit

Im Rahmen der Forderung nach Evidenzbasierung in der Medizin wird auch von der Psychotherapie der Nachweis verlangt, dass sie wirksam ist. Deshalb hat die Charta fur Psychotherapie, der schweizerische Dachverband fur psychotherapeutische Ausbildungsinstitutionen, im Jahr 2004 die Initiative ergriffen, eine prospektive, naturalistische Psychotherapie-Outcomestudie durchzufuhren. Alle der Charta angegliederten Institute wurden angefragt, sich an der Studie zu beteiligen. In der Schweiz sind nach wie vor verschiedenste psychotherapeutische Richtungen prasent. Deshalb bietet diese Studie auch die einmalige Gelegenheit zu untersuchen, ob die TherapeutInnen der verschiedenen Schulen tatsachlich die als schulenspezifisch deklarierten Techniken benutzen, oder ob es z.B. einige wenige Techniken gibt, die breit angewendet werden. Im vorliegenden Artikel werden in erster Linie das Studien-Design und deskriptive Daten der Baseline-Erhebung vorgestellt. Aus 9 verschiedenen psychotherapeutischen Instituten waren 86 Therapeuten bereit, an der Studie teilzunehmen. Sie rekrutierten insgesamt 362 PatientInnen, 238 Patientinnen und 124 Patienten im Alter zwischen 17 und 72 Jahren. Bezogen auf die 5 wichtigsten Outcome-Instrumente zeigte sich, dass 80% der PatientInnen zu Beginn der Therapie in mindestens einem Instrument eine Einschatzung im dysfunktionalen Bereich hatten. 90% der PatientInnen hatten eine Diagnose auf der Achse I des DSM IV. Weitere Auswertungen werden Outcome- und Prozess-Outcome-Ergebnisse zum Inhalt haben. Schlusselworter : Psychotherapie, Outcome-Studie, prospektiv naturalistisches Design, psychotherapeutische Techniken
Warmer Hearts, Warmer Rooms How Positive Communal Traits Increase Estimates of Ambient Temperature

Conceptual representations of warmth have been shown to be related to people's perceptions of ambient temperature. Based on this premise, we hypothesized that merely thinking about personality traits related to communion (but not agency) influences physical experience of warmth. Specifically, the three studies revealed that (a) perceptions of temperature are influenced by both positive and negative attributes within the communion but not agency dimension, (b) the effect is stronger when traits indicate sociability rather than morality subdimension of communion, and (c) communion activation affects temperature perceptions independently of target's or self- perceptions.
Run Spot Run: Capturing and Tagging Footage of a Race by Crowds of Spectators

There has been a massive growth in the number of people who film and upload amateur footage of events to services such as Facebook and Youtube, or even stream live to services such as LiveStream. We present an exploratory study that investigates the potential of these spectators in creating footage en masse; in this case, during a live trial at a local marathon. We deployed a prototype app, RunSpotRun, as a technology probe to see what kinds of footage spectators would produce. We present an analysis of this footage in terms of its coverage, quality, and contents, and also discuss the implications for a) spectators enjoying the race, and b) extracting the stories of individual runners throughout the race. We conclude with a discussion of the challenges that remain for deploying such technology at a larger scale.
Abstract—the Database Reverse Engineering Problems And

solving processes are getting mature, even though, the academic community is facing the complex problem of knowledge transfer, both in university and industrial contexts. This paper presents a new CASE tool developed at the University of Jordan which addresses an efficient support of this transfer, namely UJ-CASE-TOOL. It is a small and self-contained application exhibiting representative problems and appropriate solutions that can be understood in a limited time. It presents an algorithm that describes the developed academic CASE tool which has been used for several years both as an illustration of the principles of database reverse engineering and as an exercise aimed at academic and industrial students.
Evaluation of the Value of Fasting Plasma Glucose in the First Prenatal Visit to Diagnose Gestational Diabetes Mellitus in China

OBJECTIVE To evaluate the value of fasting plasma glucose (FPG) value in the first prenatal visit to diagnose gestational diabetes mellitus (GDM). RESEARCH DESIGN AND METHODS Medical records of 17,186 pregnant women attending prenatal clinics in 13 hospitals in China, including the Peking University First Hospital (PUFH), were examined. Patients with pre-GDM were excluded; data for FPG at the first prenatal visit and one-step GDM screening with 75-g oral glucose tolerance test (OGTT) performed between 24 and 28 weeks of gestation were collected and analyzed. RESULTS The median ± SD FPG value was 4.58 ± 0.437. FPG decreased with increasing gestational age. FPG level at the first prenatal visit was strongly correlated with GDM diagnosed at 24–28 gestational weeks (χ2 = 959.3, P < 0.001). The incidences of GDM were 37.0, 52.7, and 66.2%, respectively, for women with FPG at the first prenatal visit between 5.10 and 5.59, 5.60 and 6.09, and 6.10–6.99 mmol/L. The data of PUFH were not statistically different from other hospitals. CONCLUSIONS Pregnant women (6.10 ≤ FPG < 7.00 mmol/L) should be considered and treated as GDM to improve outcomes; for women with FPG between 5.10 and 6.09 mmol/L, nutrition and exercise advice should be provided. An OGTT should be performed at 24–28 weeks to confirm or rule out GDM. Based on our data, we cannot support an FPG value ≥5.10 mmol/L at the first prenatal visit as the criterion for diagnosis of GDM.
Tumor deposit is a poor prognostic indicator in patients who underwent simultaneous resection for synchronous colorectal liver metastases

Background Tumor deposits are one of the important influencing factors among the different editions of Tumor, Node, Metastasis classification. Incidence and prognosis of tumor deposits in stage I, II, and III colorectal cancer patients has been explored. The aim of this study was to determine the prognostic value of tumor deposits in stage IV colorectal cancer patients who underwent simultaneous resection for synchronous colorectal liver metastases (SCRLM). Methods Clinicopathological and outcome data of 146 consecutive SCRLM patients who underwent simultaneous R0 resection between July 2003 and July 2013 were collected from our prospectively established SCRLM database. The prognostic value of tumor deposits was evaluated by Kaplan–Meier and Cox regression analysis. Results Tumor deposits were detected in 41.8% (61/146) of these SCRLM patients. Tumor deposits were significantly correlated with lymph node metastasis and nerve invasion of the primary tumors (P=0.002, P=0.041; respectively). The Kaplan–Meier survival analysis revealed that the overall survival (OS) and disease-free survival (DFS) of SCRLM patients with tumor deposits were significantly poorer than those with no tumor deposits (P=0.039, P=0.001; respectively). And with multivariate analysis, we found that positive tumor deposits were significantly associated with shorter DFS independent of lymph node status (P=0.002). Subgroup analysis found that of the 57 SCRLM patients with negative lymph node status, the OS and DFS of patients with positive tumor deposits were significantly shorter than those with negative tumor deposits (P=0.002 and P=0.031, respectively). Of the 89 patients with positive lymph node status, the OS of patients with tumor deposits was not significantly different than those without tumor deposits (P=0.965); however, the DFS of patients with tumor deposits was significantly shorter than those with no tumor deposits (P=0.034). Conclusion Tumor deposits may be an independent adverse prognostic factor in SCRLM patients who underwent simultaneous R0 resection.
UBIQUITIN-SPECIFIC PROTEASE16 interacts with a HEAVY METAL ASSOCIATED ISOPRENYLATED PLANT PROTEIN27 and modulates cadmium tolerance

Protein ubiquitination and deubiquitination are two reversible processes catalyzed by ubiquitin ligases and deubiquitinating enzymes, respectively. In Arabidopsis, lots of substrates of ubiquitin ligases were found, whereas only a few targets of deubiquitinating enzymes were identified. Recently, we reported that a functional UBIQUITIN-SPECIFIC PROTEASE16 (UBP16) was involved in salt tolerance through positively regulating plasma membrane Na+/H+ antiport activity and at least partially modulating SERINE HYDROXYMETHYLTRANSFERASE1 (SHM1) stability and activity. Here, we report that UBP16 interacts with HEAVY METAL ASSOCIATED ISOPRENYLATED PLANT PROTEIN27 (HIPP27), a metallochaperone containing a predicted heavy-metal-associated domain, which has been reported to play an important role in cadmium detoxification. Meanwhile, the ubp16 mutant showed more sensitive to cadmium than wild-type. Taken together, HIPP27 may be another target of UBP16 in cadmium response.
Emerging concepts and future challenges in innate lymphoid cell biology

Innate lymphoid cells (ILCs) are innate immune cells that are ubiquitously distributed in lymphoid and nonlymphoid tissues and enriched at mucosal and barrier surfaces. Three major ILC subsets are recognized in mice and humans. Each of these subsets interacts with innate and adaptive immune cells and integrates cues from the epithelium, the microbiota, and pathogens to regulate inflammation, immunity, tissue repair, and metabolic homeostasis. Although intense study has elucidated many aspects of ILC development, phenotype, and function, numerous challenges remain in the field of ILC biology. In particular, recent work has highlighted key new questions regarding how these cells communicate with their environment and other cell types during health and disease. This review summarizes new findings in this rapidly developing field that showcase the critical role ILCs play in directing immune responses through their ability to interact with a variety of hematopoietic and nonhematopoietic cells. In addition, we define remaining challenges and emerging questions facing the field. Finally, this review discusses the potential application of basic studies of ILC biology to the development of new treatments for human patients with inflammatory and infectious diseases in which ILCs play a role.
Prostaglandins and Other Lipid Mediators eview he role of long chain fatty acids and their epoxide metabolites in ociceptive signaling

Lipid derived mediators contribute to inflammation and the sensing of pain. The contributions of omega6 derived prostanoids in enhancing inflammation and pain sensation are well known. Less well explored are the opposing anti-inflammatory and analgesic effects of the omega-6 derived epoxyeicosatrienoic acids. Far less has been described about the epoxidized metabolites derived from omega-3 long chain fatty acids. The epoxide metabolites are turned over rapidly with enzymatic hydrolysis by the soluble poxyeicosatrienoic acids (EETs) poxydocosapentanoic acids (EDP
Department of Biology

The Department of Biology (https://biology.mit.edu) oers undergraduate, graduate, and postdoctoral training in basic biology, and in a variety of biological elds of specialization. The quantitative aspects of biology, including molecular biology, biochemistry, genetics, and cell biology, represent the core of the program. Students in the department are encouraged to acquire a solid background in the physical sciences not only to master the applications of mathematics, physics, and chemistry to biology, but also to develop an integrated scientic perspective. The various programs, which emphasize practical experimentation, combine a minimum of formal laboratory exercises with ample opportunities for research work both in project-oriented laboratory subjects and in the department's research laboratories. Students at all levels are encouraged to acquire familiarity with advanced research techniques and to participate in seminar activities.
Impact of Network Dynamics on End-to-End Protocols : Case Studies in TCP and Reliable Multicast 1

End-to-end protocols measure network characteristics and react based on their estimates of network performance. Network dynamics can alter the topology significantly, and thereby affect protocol operation. Topology changes may result in routing pathologies (such as route loops, packet interleaving), changes to the end-to-end path characteristics, network partition etc, that then impact the performance of end-to-end protocols. This paper presents methodologies to evaluate an end-to-end protocol in the presence of network dynamics using a simulator. A number of models of network dynamics are introduced. In the paper, we evaluate two end-to-end protocols over dynamic topologies and study the adaptivity of these protocols to topology changes. The first part of the paper illustrates the effect of packet interleaving on the performance of TCP. The second part of the paper is a systematic evaluation of the adaptive timer mechanisms in Scalable Reliable Multicast (SRM). The timer mechanisms are evaluated under simple topology changes, as well as under network partition conditions. The paper concludes by posing a number of open research questions about the behaviour of different reliable multicast mechanisms when operating over dynamic topologies.
Stochastic GPU-based Multithread Implementation of Multiple Back-propagation

Graphics Processing Units (GPUs) have evolved into a highly parallel, multi-threaded, many-core processor with enormous computational power. The GPU is especially well suited to address pattern recognition problems that can be expressed as data-parallel computations. Thus it provides a viable alternative to the use of dedicated hardware in the neural network (NN) field, where the long training times have always been a major drawback. In this paper, we propose a GPU implementation of the online (stochastic) training mode of the Multiple BackPropagation (MBP) algorithm and compare it with corresponding standalone CPU version and with the batch training mode GPU implementation. For a fair and unbiased comparison we run the experiments with benchmarks from machine learning and pattern recognition field and we show that the GPU performance excel the CPU results in particular for high complex problems.
How identification of rhythmic categories depends on tempo and meter

Extended abstract In previous work we elaborated a way to systematically investigate the perceptual division of a continuous space of temporal patterns into discrete rhythmic categories (Aarts, Desain & Jansen, in preparation; Aarts & Jansen, 1999). We studied the perception of short rhythmical patterns by sampling the space of all possible patterns of three interonset-intervals (IOI), with a total duration of one second. For this, musicians were asked to transcribe these short patterns of three IOIs (i.e. four onsets) into music notation. It was shown that subjects were able to identify rhythmic categories as regions of the rhythm space. Next to an insight in the perception of rhythmic categories, the results are essential in the design and construction of automatic music transcription systems (see Cemgil, Desain & Kappen, in press).
Anti-arthritic activity of Fu-Fang-Lu-Jiao-Shuang on collagen-induced arthritis in Balb/c mice and its underlying mechanisms

Background: Rheumatoid arthritis (RA) is a common, autoimmune disorder characterized by progressive multiple joint destruction, deformity, disability and premature death in most patients. Fu-Fang-Lu-Jiao-Shuang (FFLJS) is an effective traditional Chinese medicine, which has long been used clinically to treat RA patients. Objective: The objective of this study is aimed to evaluate the anti-rheumatic effects of FFLJS on collagen induced arthritis (CIA) model, as well as the underlying mechanisms, which have not previously been explored. Materials and Methods: CIA was induced by immunization with type II collagen (CII) in male Balb/c mice. The mice in the onset of arthritis were treated daily with FFLJS (125 or 500 mg/kg) or 1% carboxymethyl cellulose-Na for 28 days. Paw thickness and arthritic score were evaluated to confirm the anti-arthritic effect of FFLJS on CIA in mice. Levels of anti-CII antibody, proinflammatory cytokines interleukin-1 (IL-1) β, IL-17, and tumor necrosis factor-α (TNF-α) as well as prostaglandin E-2 (PGE-2) in serum and histological changes in the ankle joint were also analyzed. In addition, expressions of matrix metalloproteinases-1 (MMP-1), MMP-3 and tissue inhibitors of matrix metalloproteases-1 (TIMP-1) in synovial tissue were also detected to further study the molecular mechanism of the anti-arthritic effects of FFLJS. Results: During therapeutic treatment, FFLJS significantly reduced paw thickness and arthritic score in CIA mice, decreased the amounts of TNF-α, IL-1 β, IL-17, PGE-2 and anti-CII antibody in serum. In addition, FFLJS treatment could prevent the bone destruction by reducing the expression of MMP-1 and MMP-3, increasing the expression of TIMP-1 in synovial tissue of CIA mice. Conclusion: These findings offer the convincing evidence for the first time that the anti-rheumatic effects of FFLJS might be related to down-regulation of TNF-α, IL-1 β, IL-17 and PGE-2 levels for acute arthritis, and regulation of MMP-1, MMP-3 and TIMP-1 protein expression for chronic arthritis.
FINITE ELEMENT METHODS FOR STOKES EQUATIONS

where u can be interpreted as the velocity field of an incompressible fluid motion, and p is then the associated pressure, the positive constant μ is the viscosity coefficient of the fluid. For simplicity, we consider homogenous Dirichlet boundary condition for the velocity, i.e. u|∂Ω = 0. To easy the understanding, we write the component-wise formulation in two dimensions. Let u = (u, v) and f = (f1, f2). Then equations (1)-(2) consists of three equations −μ∆u+ ∂xp = f1, −μ∆v + ∂yp = f2, ∂xu+ ∂yv = 0.
Ambient recommendations in the pop-up shop

In this paper we present the design and first-stage analysis of a purposely built, smart, pop-up wine shop. Our shop learns from visitors' choices and recommends wine using collaborative filtering and ambient feedback displays integrated into its furniture. Our ambient recommender system was tested in a controlled laboratory environment. We report on the qualitative feedback and between subjects study, testing the influence the system had in wine choice behavior. Participants reported the system helpful, and results from our empirical analysis suggest it influenced buying behavior.