gebhart/patrepeval huggingface dataset:
Supplementary Table S3 from Heterogeneity in <i>NECTIN4</i> Expression Across Molecular Subtypes of Urothelial Cancer Mediates Sensitivity to Enfortumab Vedotin (2023)

&lt;p&gt;The p values from pairwise comparisons amongst the molecular subtypes for each cohort using the Wilcoxon rank-sum test are shown.&lt;/p&gt;
Adrenomedullin-CALCRL axis controls relapse-initiating drug tolerant acute myeloid leukemia cells (2021)

Drug tolerant/resistant leukemic stem cell (LSC) subpopulations may explain frequent relapses in acute myeloid leukemia (AML), suggesting that these relapse-initiating cells (RICs) persistent after chemotherapy represent bona fide targets to prevent drug resistance and relapse. We uncover that calcitonin receptor-like receptor (CALCRL) is expressed in RICs, and that the overexpression of CALCRL and/or of its ligand adrenomedullin (ADM), and not CGRP, correlates to adverse outcome in AML. CALCRL knockdown impairs leukemic growth, decreases LSC frequency, and sensitizes to cytarabine in patient-derived xenograft models. Mechanistically, the ADM-CALCRL axis drives cell cycle, DNA repair, and mitochondrial OxPHOS function of AML blasts dependent on E2F1 and BCL2. Finally, CALCRL depletion reduces LSC frequency of RICs post-chemotherapy in vivo. In summary, our data highlight a critical role of ADM-CALCRL in post-chemotherapy persistence of these cells, and disclose a promising therapeutic target to prevent relapse in AML.
A Direct Assay for Measuring Free 25-Hydroxyvitamin D (2017)

Recent studies suggest that the concentration and genotype of vitamin D binding protein (VDBP) are important factors that determine the bioavailability of 25-hydroxyvitamin D [25(OH)D] in blood. Accumulating data indicate that, e.g., in pregnant women, hemodialysis patients, chronic kidney disease, liver failure, and bladder and pancreatic cancers, the measurement of free 25(OH)D in serum provides more relevant diagnostic information than measurement of total 25(OH)D. The aim of this study was to develop and validate an ELISA for direct measurement of free 25(OH)D in serum. A simple and direct ELISA was developed, based on a two-step immunoassay procedure performed in a microtiter plate. The assay has been characterized in terms of precision (4-10% CV, according to concentration), sensitivity (limits of blank = 0.5-1.0 pg/mL and LODs = 1.3-1.8 pg/mL), accuracy (correlation to dialysis, ELISA = 0.99xdialysis-0.5 pg/mL, r2 = 0.74), cross-reactivity of the antibody for the D2 form (77%), and addition of both VDBP and albumin (35-38% recovery upon addition of VDBP, 53-58% upon addition of albumin). The assay has already been used in multiple studies, including its comparison with calculation methods and in studies of patients with liver failure, different ethnic groups, supplemented mice, respiratory diseases, and obesity. The free 25(OH)D ELISA can be used in studies as a valuable tool to establish the clinical relevance of free 25(OH)D.
Leadership team cohesiveness and team performance (2006)

Purpose To examine leadership style (transactional versus transformational), knowledge level, and team cohesiveness as antecedents of team performance. Design/methodology/approach The study was conducted among students studying for an MBA. The 252 participant students were involved in a computerized business simulation course which required forming teams of about six members. Each team represented the management of one firm that competed with the other groups. Findings Transformational leadership was associated with a higher level of team cohesiveness, as compared to transactional leadership. Both knowledge level and team cohesiveness predict team performance, particularly among men. Research limitations/implications The student sample may not necessarily represent responses from workers in an actual organization. From a measurement perspective, the reliability of the one item scale of leadership could not be ascertained. Practical implications For improving team performance, a manager should enhance team knowledge and encourage greater team cohesiveness. Originality/value Using a simulated research design, leadership style, an antecedent associated with individual performance, was also found to be related to team performance.
A 12-bit, 200MS/s digitally calibrated pipeline ADC with Embedded Sample and Hold (2014)

This paper introduces a 12-bit pipeline Analog to Digital Converter (ADC) using 1.2V and 0.13μm CMOS technology. The first stage utilizes the Embedded Sample and Hold technique to eliminate the dedicated power hungry Sample and Hold circuit. Low gain Opamps are used with a Foreground Digital Calibration scheme to account for the Opamp's finite gain and non-linearity. The ADC consumes 65 mW and achieves a maximum SNDR of 68.5 dB with an SFDR up to 80 dB which corresponds to a Figure of Merit (FOM) of about 160 fJ/step.
Joint end-to-end loss-delay hidden Markov model for periodic UDP traffic over the Internet (2006)

Performance of real-time applications on network communication channels is strongly related to losses and temporal delays. Several studies showed that these network features may be correlated and exhibit a certain degree of memory such as bursty losses and delays. The memory and the statistical dependence between losses and temporal delays suggest that the channel may be well modeled by a hidden Markov model (HMM) with appropriate hidden variables that capture the current state of the network. In this paper, an HMM is proposed that shows excellent performance in modeling typical channel behaviors in a set of real packet links. The system is trained with a modified version of the Expectation-Maximization (EM) algorithm. Hidden-state analysis shows how the state variables characterize channel dynamics. State-sequence estimation is obtained by the use of Viterbi algorithm. Real-time modeling of the channel is the first step to implement adaptive communication strategies.
Degradation pathway of CopA, the antisense RNA that controls replication of plasmid R1 (1998)

RNA decay in bacteria is carried out by a number of enzymes that participate in the coordinated degradation of their substrates. Endo- and exonucleolytic cleavages as well as polyadenylation are generally involved in determining the half-life of RNAs. Small, untranslated antisense RNAs are suitable model systems to study decay. A study of the pathway of degradation of CopA, the copy number regulator RNA of plasmid R1, is reported here. Strains carrying mutations in the genes encoding RNase E, polynucleotide phosphorylase (PNPase), RNase II and poly(A) polymerase I (PcnB/PAP I)--alone or in combination--were used to investigate degradation patterns and relative half-lives of CopA. The results obtained suggest that RNase E initiates CopA decay. Both PNPase and RNase II can degrade the major 3'-cleavage product generated by RNase E. This exonucleolytic degradation is aided by PcnB, which may imply a requirement for A-tailing. RNase II can partially protect CopA's 3'-end from PNPase-dependent degradation. Other RNases are probably involved in decay, since in rnb/pnp double mutants, decay still occurs, albeit at a reduced rate. Experiments using purified RNase E identified cleavage sites in CopA in the vicinity of, but not identical to, those mapped in vivo, suggesting that the cleavage site specificity of this RNase is modulated by additional proteins in the cell. A model of CopA decay is presented and discussed.
Rearrangement of bridging alkylidyneiron complexes to bridging alkenyliron complexes (1983)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTRearrangement of bridging alkylidyneiron complexes to bridging alkenyliron complexesCharles P. Casey, Seth R. Marder, and Paul J. FaganCite this: J. Am. Chem. Soc. 1983, 105, 24, 7197–7198Publication Date (Print):November 1, 1983Publication History Published online1 May 2002Published inissue 1 November 1983https://pubs.acs.org/doi/10.1021/ja00362a044https://doi.org/10.1021/ja00362a044research-articleACS PublicationsRequest reuse permissionsArticle Views43Altmetric-Citations13LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
SmoothGrad: removing noise by adding noise (2017)

Explaining the output of a deep network remains a challenge. In the case of an image classifier, one type of explanation is to identify pixels that strongly influence the final decision. A starting point for this strategy is the gradient of the class score function with respect to the input image. This gradient can be interpreted as a sensitivity map, and there are several techniques that elaborate on this basic idea. This paper makes two contributions: it introduces SmoothGrad, a simple method that can help visually sharpen gradient-based sensitivity maps, and it discusses lessons in the visualization of these maps. We publish the code for our experiments and a website with our results.
The role of Frizzled-4 mutations in familial exudative vitreoretinopathy and Coats disease (2010)

The authors identified 12 FEVR probands with FZD4 mutations. FZD4 mutation screening can be a useful tool especially in mild or atypical cases of FEVR. Germ-line mutations in FZD4 do not appear to be a common cause of Coats disease.
Digital closed loop design for wideband envelope tracking system (2014)

In this paper, we will show two methods of digital closed loop envelope tracking systems for high bandwidth communication systems, tested on wifi 80 MHz signals (11ac) in high level simulation platform (matlab & simulink). We will present the challenges of high frequency digital DC2DC converter for envelope tracking (ET) as load modulation wide digital controller loop and noise and saturation in the loop, and multilevel ET based on several high BW digital low dropout (DLDO) voltage regulators, and examine the differences in terms of the challenges and coping mechanisms each one holds. We will show that although the existing highly non-linear PA in our system, both architectures provide the solution in terms of band edge (BE) mask limitation, with efficiency of ~80% for the ET full driver. All components in both architectures are fully digital and synthesizable, which has a big advantage compared to analog options in efficiency noise and size, and of course assures robustness and flexibility.
Domain Adaptation for Image Dehazing (2020)

Image dehazing using learning-based methods has achieved state-of-the-art performance in recent years. However, most existing methods train a dehazing model on synthetic hazy images, which are less able to generalize well to real hazy images due to domain shift. To address this issue, we propose a domain adaptation paradigm, which consists of an image translation module and two image dehazing modules. Specifically, we first apply a bidirectional translation network to bridge the gap between the synthetic and real domains by translating images from one domain to another. And then, we use images before and after translation to train the proposed two image dehazing networks with a consistency constraint. In this phase, we incorporate the real hazy image into the dehazing training via exploiting the properties of the clear image (e.g., dark channel prior and image gradient smoothing) to further improve the domain adaptivity. By training image translation and dehazing network in an end-to-end manner, we can obtain better effects of both image translation and dehazing. Experimental results on both synthetic and real-world images demonstrate that our model performs favorably against the state-of-the-art dehazing algorithms.
Exploring student challenges in an online project-based course (2022)

In addition to sound technical skills, industry jobs require soft skills such as teamwork and good organizational abilities. This is even more important in today's landscape, where working from the office is substituted with working from home. This trend, together with the shift towards distributed teams that are separated geographically and across time zones is expected to create challenges addressed through improved management and soft skills. Organizations of higher learning include the development of capstone or team projects as part of their curricula in order to prepare students for collaborative work and improve their organizational abilities. In this paper, we present an exploratory study focused on the challenges encountered by students in two consecutive iterations of a Team Projects course. The second iteration took place fully online due to the ongoing pandemic. We discovered the lack of face to face communication and schedule synchronization as some of the important challenges reported. We show that mitigating strategies by both teaching staff and the students themselves helped keep communication open and engagement high. We provide a replication package that allows repeating or extending our study.
Pericardial tamponade caused by Pasteurella multocida infection after a cat bite (2001)

An unusual case of meningitis and pericardial tamponade caused by Pasteurella multocida after a cat bite is reported. The patient was successfully treated by antibiotics and pericardiocentesis and made an uneventful recovery from a life threatening condition. This case illustrates the potential dangers that can arise from a seemingly trivial and commonplace injury.
Metformin therapy and clinical uses (2008)

Metformin is now established as a first-line antidiabetic therapy for the management of type 2 diabetes. Its early use in treatment algorithms is supported by lack of weight gain, low risk of hypoglycaemia and its mode of action to counter insulin resistance. The drug's anti-atherosclerotic and cardioprotective effects have recently been confirmed in prospective and retrospective studies, and appear to reflect a collection of glucose-independent effects on the vascular endothelium, suppressant effects on glycation, oxidative stress and formation of adhesion molecules, stimulation of fibrinolysis and favourable effects on the lipid profile. Although avoidance of troublesome gastrointestinal tolerability issues requires careful dose titration, the risk of serious adverse events is considered low provided that contra-indications (especially with respect to renal function) are observed. As many of its actions go beyond glucose lowering, emerging evidence indicates potential benefits in other insulin-resistant states and possibly tumour suppression.
Ant Brood Clustering on Intel Xeon Multi-core: Challenges and Strategies (2018)

Swarm intelligence algorithms such as ant colony optimization (ACO) and particle swarm optimization (PSO) are computationally intensive. Ant Brood Clustering (ABC) algorithm is one of the techniques in the family of ant algorithms. It is based on how ants cluster their brood or corpse into different piles. ABC has been efficiently used in solving the clustering problem in data analytics. However, they are computationally intensive. In this paper, we explore and evaluate eight parallel strategies of the ant brood clustering algorithm on Intel Xeon multi-core shared memory machine exploiting algorithm level and program level parallelism. A speedup of 25.3x is achieved with 56 hardware threads on dual 14 core Intel Xeon shared memory machine with coarse-grained, data level protection strategy. We show that contrary to other swarm intelligence techniques, fine grained parallelism is not suitable for this algorithm.
Hierarchical sparse coded surface models (2014)

In this paper, we describe a novel approach to construct textured 3D environment models in a hierarchical fashion based on local surface patches. Compared to previous approaches, the hierarchy enables our method to represent the environment with differently sized surface patches. The reconstruction scheme starts at a coarse resolution with large patches and in an iterative fashion uses the reconstruction error to guide the decision as to whether the resolution should be refined. This leads to variable resolution models that represent areas with few variations at low resolution and areas with large variations at high resolution. In addition, we compactly describe local surface attributes via sparse coding based on an overcomplete dictionary. In this way, we additionally exploit similarities in structure and texture, which leads to compact models. We learn the dictionary directly from the input data and independently for every level in the hierarchy in an unsupervised fashion. Practical experiments with large-scale datasets demonstrate that our method compares favorably with two state-of-the-art techniques while being comparable in accuracy.
Molecular and physiological manifestations and measurement of aging in humans (2017)

Biological aging is associated with a reduction in the reparative and regenerative potential in tissues and organs. This reduction manifests as a decreased physiological reserve in response to stress (termed homeostenosis) and a time-dependent failure of complex molecular mechanisms that cumulatively create disorder. Aging inevitably occurs with time in all organisms and emerges on a molecular, cellular, organ, and organismal level with genetic, epigenetic, and environmental modulators. Individuals with the same chronological age exhibit differential trajectories of age-related decline, and it follows that we should assess biological age distinctly from chronological age. In this review, we outline mechanisms of aging with attention to well-described molecular and cellular hallmarks and discuss physiological changes of aging at the organ-system level. We suggest methods to measure aging with attention to both molecular biology (e.g., telomere length and epigenetic marks) and physiological function (e.g., lung function and echocardiographic measurements). Finally, we propose a framework to integrate these molecular and physiological data into a composite score that measures biological aging in humans. Understanding the molecular and physiological phenomena that drive the complex and multifactorial processes underlying the variable pace of biological aging in humans will inform how researchers assess and investigate health and disease over the life course. This composite biological age score could be of use to researchers seeking to characterize normal, accelerated, and exceptionally successful aging as well as to assess the effect of interventions aimed at modulating human aging.
One-Step Electrochemical Deposition of Cu-In-Ga Mixed Oxide Thin Films for Low-Cost CIGS Solar Cells (2012)

One step electrodeposition of mixed copper indium gallium oxides and hydroxides film has been carried out by cathodic deposition from dissolved metallic salts in nitrate electrolyte. The deposition conditions allow to control the composition of the film and the proportion of metallic elements in the optimal range for CIGS. The precursor films are then reduced into mixed metallic film by thermal annealing in an hydrogen containing atmosphere and then transformed in CIGS by selenization with elemental selenium. Cell efficiency of 9.4% has been obtained with this process.
Structures of the σ2 receptor enable docking for bioactive ligand discovery (2024)

The σ2 receptor has attracted intense interest in cancer imaging1, psychiatric disease2, neuropathic pain3–5 and other areas of biology6,7. Here we determined the crystal structure of this receptor in complex with the clinical candidate roluperidone2 and the tool compound PB288. These structures templated a large-scale docking screen of 490 million virtual molecules, of which 484 compounds were synthesized and tested. We identified 127 new chemotypes with affinities superior to 1 μM, 31 of which had affinities superior to 50 nM. The hit rate fell smoothly and monotonically with docking score. We optimized three hits for potency and selectivity, and achieved affinities that ranged from 3 to 48 nM, with up to 250-fold selectivity versus the σ1 receptor. Crystal structures of two ligands bound to the σ2 receptor confirmed the docked poses. To investigate the contribution of the σ2 receptor in pain, two potent σ2-selective ligands and one potent σ1/σ2 non-selective ligand were tested for efficacy in a mouse model of neuropathic pain. All three ligands showed time-dependent decreases in mechanical hypersensitivity in the spared nerve injury model9, suggesting that the σ2 receptor has a role in nociception. This study illustrates the opportunities for rapid discovery of in vivo probes through structure-based screens of ultra large libraries, enabling study of underexplored areas of biology.
0140 CO-LOCALIZATION OF SEROTONIN AND CANNABINOID RECEPTORS IN THE NODOSE GANGLIA (2017)

Pharmacological treatments for obstructive sleep apnea are limited due to incomplete knowledge of the neurochemical properties of respiratory circuits. The afferent vagus nerves provide key respiratory modulating feedback to the brainstem. The nodose ganglia (NG) of the vagus nerves are neurochemically diverse containing many receptors, including serotonin type 3 receptors (5-HT3), and cannabinoid type 1 (CB1) and/or type 2 (CB2) receptors. In anesthetized rats, a cannabinoid (CB) agonist attenuates serotonin (5-HT)-induced reflex apnea via activation of CB receptors located on the NG. However, it is unclear how 5-HT3 receptors colocalize with CB1 and CB2 receptors. Here, we examine the localization of these three receptors in the rat NG. NG were extracted from anesthetized adult male Sprague-Dawley rats, fixed with 4% paraformaldehyde and 20% sucrose, processed and embedded in paraffin and sectioned using a microtome. Sections were covered with primary antibodies for 5-HT3 and CB1 receptors or 5-HT3 and CB2 receptors. After rinsing the sections were covered with fluorescent secondary antibodies. The sections were rinsed and coverslipped with anti-fade glycerol. The immunohistochemical specificity was verified by omitting the primary antibodies. The slides were scanned using a Vectra automated quantitative pathology imaging system. Data are presented as mean ± SEM of percentage of fluorescent pixels observed for the entire sectioned ganglion. The NG were 31.37 ± 5.8% fluorescent for 5-HT3 receptors. A tiny percentage of the NG was fluorescent for CB1 (0.03 ± 0.02%) or CB2 (0.03 ± 0.01%) receptors. Colocalization of 5-HT3 and CB1, or 5-HT3 and CB2, was 0.03 ± 0.01% or 0.03 ± 0.01%. In other words, those NG cells that expressed CB receptors also expressed 5-HT3 receptors. Only a small percentage of NG cells express CB receptors, and most of those cells are colocalized with 5-HT3. This work was supported by the Chicago Biomedical Consortium Postdoctoral Research Grant Program.
Estimation of systolic blood pressure from the second heart sounds (2002)

The second heart sound signal is modelled using exponentially damping sinusoids and forward linear predictions. Relationships between the parameters of the model and systolic blood pressure in the aortic root are investigated. Damping and amplitude parameters show higher (statistically significant) correlation to the systolic pressure.