gebhart/patrepeval huggingface dataset:
Gene expression profile of human endothelial cells exposed to sustained fluid shear stress (2002)

Biomechanical forces can modulate endothelial phenotype through changes in gene expression. We hypothesized that physiological laminar shear stresses (LSS) act as differentiative stimuli on endothelial cells (EC) to alter gene expression, creating an antioxidant, anti-apoptotic and anti-proliferative environment. The transcriptional profile of cultured human umbilical vein endothelial cells (HUVEC) exposed to LSS was evaluated by GeneCalling; 107 genes demonstrated at least a twofold change in expression at 24 h (LSS vs. static). These flow-responsive genes represent a limited number of functional clusters that include transcription factors, antioxidants, signaling molecules, cell cycle regulators, and genes involved in cellular differentiation. Immunohistochemistry and in situ hybridization confirmed that many of these flow-responsive genes, including the novel basic helix-loop-helix transcription factor Hath6, are expressed in EC in vivo. Thus these data identify a limited set of flow-responsive genes expressed in the endothelium that may be responsible for the establishment and maintenance of the flow-adapted endothelial phenotype in vivo.
Markerless Full Body Shape and Motion Capture from Video Sequences (2002)

Reference CVLAB-CONF-2002-006 URL: http://cvlab.epfl.ch/publications/publications/2002/FuaGDR02.pdf Record created on 2006-02-03, modified on 2017-05-12
The translocation t(1;22)(p13;q13) is a nonrandom marker specifically associated with acute megakaryocytic leukemia in young children (1992)

Abstract We present the nonrandom occurrence, frequency, and degree of immunophenotype association of the t(1;22)(p13;q13) in children with acute nonlymphocytic leukemia (ANLL). This karyotype anomaly occurred in leukemia cells from five of 445 (1.1%) children with newly diagnosed ANLL who were successfully studied by cytogenetic analysis at four European centers between January 1987 and January 1992. The occurrence of the t(1;22) was restricted to the French-American-British classification (FAB) subtype M7. The overall incidence in children with acute megakaryocytic leukemia (AMKL) was 27.8% (5/18 cases); in infants with AMKL, the frequency of the t(1;22) was 66.7% (4/6 cases). Three of the patients carrying this anomaly had a diploid karyotype, whereas in two cases a hyperdiploid karyotype was found. However, in all five patients, the t(1;22) was the only translocation event present at diagnosis. All patients received aggressive chemotherapy for acute myelogenous leukemia (AML). Two patients died within 15 months of diagnosis without entering remission. One of three patients who entered remission died 7 months after diagnosis, most likely from intramedullar hemorrhage. Only two of the five children with the t(1;22) who received autologous bone marrow transplantation (BMT) are alive and in complete remission (CR) 23 and 40 months after diagnosis, respectively. At the time of diagnosis, the age of the oldest child carrying the t(1;22) was 18 months. The cases with this chromosome anomaly were compared with an age-matched group of five children with AMKL lacking this translocation. The patients with the t(1;22) had a lower median value of the peripheral white blood cell (WBC) count and a higher median hemoglobin level than the patients from the matched group. In the latter cases, normocellular or hypercellular bone marrow (BM) was detected at diagnosis. In contrast, all children with the t(1;22) in our series had a hypocellular BM. Histological BM analyses were available in three of these patients and showed marked fibrosis. Other clinical and laboratory parameters showed no obvious differences between the matched groups. Despite intensive chemotherapy, AMKL in children appears to be associated with a poor prognosis. The clinical courses of the children with AMKL and the t(1;22) presented may be indicative of a beneficial effect of autologous BMT in this subset of patients.
A low dropout voltage regulator with a transient voltage spikes reducer and improved figure of merit (2019)

An area efficient output capacitor-free low dropout [LDO] voltage regulator with an improved figure of merit is presented in this paper. The proposed LDO regulator consists of a novel, dynamically biased error amplifier that reduces overshoot and undershoot voltage spikes arising from abrupt load changes. Source bulk modulation is employed to enhance the current driving capability of the pass transistor. An adaptive biasing scheme is also used along with dynamic biasing to improve the current efficiency of the system. The on-chip capacitor required for proper working of the LDO regulator is only 35 pF. The proposed LDO regulator is designed and simulated in 180 nm standard CMOS technology. The LDO regulator exhibits a line regulation of 1.67 mV$\mathbin{/}$V and a load regulation of 100 $\mu {V}\mathbin{/}$mA. When load changes from 0 mA to 100 mA in 1 $\mu $s, an undershoot of 148 mV and an overshoot of 172 mV are observed. The measured power supply rejection ratio is 25 dB at 100 kHz. The working of the proposed LDO regulator has been tested under all process corners and Monte-Carlo statistical analysis reveals that it is robust against process variations and local mismatch.
High-Pressure Inactivation of Human Norovirus Virus-Like Particles Provides Evidence that the Capsid of Human Norovirus Is Highly Pressure Resistant (2012)

Human norovirus (NoV) is the leading cause of nonbacterial acute gastroenteritis epidemics worldwide. High-pressure processing (HPP) has been considered a promising nonthermal processing technology to inactivate food- and waterborne viral pathogens. Due to the lack of an effective cell culture method for human NoV, the effectiveness of HPP in inactivating human NoV remains poorly understood. In this study, we evaluated the effectiveness of HPP in disrupting the capsid of human NoV based on the structural and functional integrity of virus-like particles (VLPs) and histo-blood group antigen (HBGA) receptor binding assays. We found that pressurization at 500 to 600 MPa for 2 min, a pressure level that completely inactivates murine norovirus and feline calicivirus, was not sufficient to disrupt the structure and function of human NoV VLPs, even with a holding time of 60 min. Degradation of VLPs increased commensurate with increasing pressure levels more than increasing time. The times required for complete disruption of human NoV VLPs at 700, 800, and 900 MPa were 45, 15, and 2 min, respectively. Human NoV VLPs were more resistant to HPP in their ability to bind type A than type B and O HBGAs. Additionally, the 23-nm VLPs appeared to be much more stable than the 38-nm VLPs. Taken together, our results demonstrated that the human NoV capsid is highly resistant to HPP. While human NoV VLPs may not be fully representative of viable human NoV, destruction of the VLP capsid is highly suggestive of a typical response for viable human NoV.
TIRF microscopy evanescent field calibration using tilted fluorescent microtubules (2009)

Total internal reflection fluorescence microscopy has become a powerful tool to study the dynamics of sub-cellular structures and single molecules near substrate surfaces. However, the penetration depth of the evanescent field, that is, the distance at which the excitation intensity has exponentially decayed to 1/e, is often left undetermined. This presents a limit on the spatial information about the imaged structures. Here, we present a novel method to quantitatively characterize the illumination in total internal reflection fluorescence microscopy using tilted, fluorescently labelled, microtubules. We find that the evanescent field is well described by a single exponential function, with a penetration depth close to theoretically predicted values. The use of in vitro reconstituted microtubules as nanoscale probes results in a minimal perturbation of the evanescent field; excitation light scattering is eliminated and the refractive index of the sample environment is unchanged. The presented method has the potential to provide a generic tool for in situ calibration of the evanescent field.
Male Sterility in Soybean -- An Overview (1988)

The most common type of reproductive mutations observed in the soybean [Glycine max (L.) Merr.] are those that induce male sterility. The high frequency of occurrence of male-sterile mutations indicates that a number of genes influence the processes of microgametogenesis and microsporogenesis. The current knowledge of these mutations is summarized. The origins of male-sterile mutations, their inheritance patterns, and known linkage relationships are detailed. The phenotypic expression of male-sterile mutations, including their effects on both male and female reproduction, is discussed. The influence of environment on the expressivity of male-sterile mutations, and the effects of male-sterile mutations on physiological processes (senescence and nitrogen fixation) are summarized. Male-sterile mutations have been useful in the study of soybean reproduction, genetic and cytogenetic investigations, and in evaluating the potential for commercial production of hybrid soybeans. These various applications of male-sterile mutations are presented.
Controllable Construction of Carbohydrate Microarrays by Site-Directed Grafting on Self-Organized Porous Films (2010)

Carbohydrate-protein interactions are critical in many biological processes. However, the interactions between individual carbohydrates and proteins are often of low affinity and difficult to study. Recent development of carbohydrate microarrays provides an effective tool to explore the interaction. In this work, carbohydrate microarrays were controllably constructed by grafting of a carbohydrate-containing monomer on self-organized honeycomb-patterned films. The films were prepared from an amphiphilic block copolymer, poly(styrene-block-(2-hydroxyethyl methacrylate)), by a breath figure method. Three-dimensional fluorescence results demonstrate that the hydroxyl groups aggregate mainly inside the pores, which afford a chance of site-directed surface modification. 2-(2,3,4,6-Tetra-O-acetyl-beta-D-glucosyloxy)ethyl methacrylate was selectively grafted in the pores by a surface-initiated atom transfer radical polymerization. Characterization by attenuated total reflectance Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy, scanning electron microscopy, atomic force microscopy, and contact angle measurements confirms the site-directed growth of the glycopolymer chains. Further specific recognition of the carbohydrate microarrays to lectin (concanavalin A) leads to an organized microarray of protein, and hence this approach also opens a new route to fabricating other functional microarrays such as protein-patterned surfaces.
Synthesis and Characterizations of In Situ Cross-Linkable Gelatin and 4-Arm-PPO-PEO Hybrid Hydrogels via Enzymatic Reaction for Tissue Regenerative Medicine (2012)

In situ cross-linkable hybrid hydrogels composed of gelatin and 4-arm-polypropylene oxide-polyethylene oxide (Tetronic) was developed as an injectable scaffold for tissue regeneration. The gelatin was modified by hydroxyphenyl propionic acid (HPA) and the Tetronic was conjugated with tyramines (Tet-TA). The hydrogels were rapidly formed by mixing the polymer solutions containing horseradish peroxidase (HRP) and hydrogen peroxide (H(2)O(2)). The gelation time and mechanical properties of the hydrogels could be controlled by varying the HRP and H(2)O(2) concentrations. In vitro degradation study of the hybrid hydrogels was carried out using collagenase and the prolonged proteolytic degradation was obtained due to the presence of the Tetronic. Human dermal fibroblast (hDFB) was cultured in the hydrogel matrices to evaluate the cyto-compatibility. The encapsulated cells were shown to be highly viable and spread over the gel matrices, suggesting that the hybrid hydrogels have an excellent cyto-compatibility. The hydrogels were also subcutaneously injected in the back of mice and the results demonstrated that the hydrogels were rapidly formed at the injected site. From these results, we demonstrate that the in situ cross-linkable hydrogels formed by hybridization of gelatin and Tetronic via enzyme-mediated reactions hold great promise for use as injectable matrices for tissue regenerative medicine due to their tunable physico-chemical properties and excellent bioactivity.
Introducing 'Socrative' as a formative assessment tool in undergraduate medical curriculum (2020)

Objective: This study aims to introduce Socrative (an online audience response system) as a formative assessment tool in undergraduate medical curriculum and to assess the attitude and perceptions of the students regarding the same. Methods: It was a questionnaire based cross sectional study conducted for 6 months in 2019 using a free version of Socrative. Quizzes were prepared and used as formative assessment to assess students’ learning of the physiology content delivered in the modules of Special senses (Year II), Respiratory system (Year I) and Cardiovascular System (Year I) at Shifa College of Medicine. Students’ survey was carried out online, at the end of the quiz to record the perceptions of Socrative as an assessment tool. Data was analysed using SPSS-21. Descriptive statistics were applied, p<0.05 was considered significant. For qualitative variables, frequency and percentage were determined and for quantitative variables, mean and standard deviation were determined. Test of association applied was independent sample t-test (for quantitative variables). Results: Students reported a higher mean scoring preference for Socrative based exam (50%) compared to the traditional paper based exam (37.1%). Majority (83.9%) of the students evaluated Socrative as a user friendly tool, saves time and resources (86.6%) and provides immediate feedback (88.7%). A good number of students suggested conducting more Socrative based assessments in future (75.8%). Conclusion: Using Socrative as a tool for formative assessment helps in providing timely and effective feedback, thereby enabling the students to reflect on their performance and focus on important concepts.
Pak J Physiol 2020;16(2):21−5
Methionyl-tRNA synthetase. (2001)

Methionyl-tRNA synthetase (MetRS) belongs to the family of 20 enzymes essential for protein biosynthesis. It links covalently methionine with its cognate tRNA. Crystal structures solved for bacterial MetRSs have given a number of interesting insights into enzyme architecture and methionylation catalysis. A comparison of sequences of MetRSs belonging to all kingdoms of life, as well as numerous biochemical and genetic studies have revealed the presence of various additional domains appended to the catalytic core of synthetase. They are responsible for interactions with tRNA and proteins. Tertiary structure of C-terminal tRNA-binding appendices can be deduced from those determined for their homologues: tRNA binding protein 111 and endothelial monocyte-activating polypeptide II. Contacts between MetRS and other proteins could be mediated not only by noncatalytic peptides but also by structural elements present in the catalytic core, e.g. Arg-Gly-Asp (RGD) motifs. Additional activities involve MetRS in the maintenance of translational fidelity and in coordination of ribosome biogenesis with protein synthesis.
Myeloperoxidase genetic polymorphism and lung cancer risk. (1997)

Myeloperoxidase is a lysosomal enzyme found in high concentrations in human lung due to recruitment of neutrophils. Myeloperoxidase activates benzo[a]pyrene as well as aromatic amines in tobacco smoke and generates carcinogen-free radicals. A single base substitution (G to A) in the promoter region of the myeloperoxidase gene has recently been demonstrated to markedly reduce transcription. We developed an RFLP/PCR assay to test the hypothesis that the allele favoring lower transcription (A allele) reduces the risk of lung cancer. Among population controls, 7.8% of 459 Caucasians and 9.4% of 244 African-Americans inherited two copies of the A allele. Caucasians with the A/A genotype were at 70% reduced risk of lung cancer (odds ratio, 0.30; 95% confidence interval, 0.10-0.93; P = 0.04; 182 cases). A lesser reduction in risk was observed for African-Americans with this genotype (odds ratio, 0.61; 95% confidence interval, 0.26-1.41; 157 cases). Individuals who inherit two copies of an allele that reduces transcription of the myeloperoxidase gene may be at decreased risk of lung cancer.
Production industrielle de microalgues et de cyanobactéries (2017)

La production de microalgues et de cyanobactéries requiert des technologies différentes de celles de l’industrie fermentaire, suite notamment à la contrainte de la lumière. En effet, les procédés retenus doivent permettre la croissance photosynthétique indispensable à l’assimilation des nutriments.
Switching to dual/monotherapy determines an increase in CD8+ in HIV-infected individuals: an observational cohort study (2018)

We found an increase in CD8 lymphocytes in people who were switched to dual regimens compared to those who were switched to triple. Patients on monotherapy did not show significant differences. The long-term implications of this difference should be ascertained.
Single-photon-counting hotspot detector with integrated RSFQ readout electronics (1999)

Absorption of an infrared photon in an ultrathin film (such as 10-nm NbN) creates a localized nonequilibrium hotspot on the submicron length scale and sub-ns time scale. If a strip /spl sim/1 /spl mu/m wide is biased in the middle of the superconducting transition, this hotspot will lead to a resistance pulse with amplitude proportional to the energy of the incident photon. This resistance pulse, in turn, can be converted to a current pulse and inductively coupled to a SQUID amplifier with a digitized output, operating at 4 K or above. A preliminary design analysis indicates that this data can be processed on-chip, using ultrafast RSFQ digital circuits, to obtain a sensitive infrared detector for wavelengths up to 10 /spl mu/m and beyond, with bandwidth of 1 GHz, that counts individual photons and measures their energy with 25 meV resolution. This proposed device combines the speed of a hot-electron bolometer with the single-photon-counting ability of a transition-edge microcalorimeter, to obtain an infrared detector with sensitivity, speed, and spectral selectivity that are unmatched by any alternative technology.
High-resolution CMOS MEA platform to study neurons at subcellular, cellular, and network levels (2015)

Studies on information processing and learning properties of neuronal networks would benefit from simultaneous and parallel access to the activity of a large fraction of all neurons in such networks. Here, we present a CMOS-based device, capable of simultaneously recording the electrical activity of over a thousand cells in in vitro neuronal networks. The device provides sufficiently high spatiotemporal resolution to enable, at the same time, access to neuronal preparations on subcellular, cellular, and network level. The key feature is a rapidly reconfigurable array of 26 400 microelectrodes arranged at low pitch (17.5 μm) within a large overall sensing area (3.85 × 2.10 mm(2)). An arbitrary subset of the electrodes can be simultaneously connected to 1024 low-noise readout channels as well as 32 stimulation units. Each electrode or electrode subset can be used to electrically stimulate or record the signals of virtually any neuron on the array. We demonstrate the applicability and potential of this device for various different experimental paradigms: large-scale recordings from whole networks of neurons as well as investigations of axonal properties of individual neurons.
ChemInform Abstract: Synthesis and Anthelmintic Activity of 3,6‐Disubstituted‐7H‐s‐triazolo(3,4‐b)(1,3,4)thiadiazines. (2001)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Dynamic Programming for Linear-Time Incremental Parsing (2010)

Incremental parsing techniques such as shift-reduce have gained popularity thanks to their efficiency, but there remains a major problem: the search is greedy and only explores a tiny fraction of the whole space (even with beam search) as opposed to dynamic programming. We show that, surprisingly, dynamic programming is in fact possible for many shift-reduce parsers, by merging “equivalent ” stacks based on feature values. Empirically, our algorithm yields up to a five-fold speedup over a state-of-the-art shift-reduce dependency parser with no loss in accuracy. Better search also leads to better learning, and our final parser outperforms all previously reported dependency parsers for English and Chinese, yet is much faster. 1
Bisphosphonate Conjugation to Proteins as a Means To Impart Bone Affinity (2000)

Growth factors are endogenous proteins capable of stimulating new bone formation, but their clinical benefit for systemic stimulation of bone mass has not been demonstrated. The critical challenge is to deliver a significant dose of the proteins to bone after intravenous injection. This challenge may be overcome by derivatizing proteins with ligands that exhibit a high bone affinity (e.g., bisphosphonates). To demonstrate the feasibility of this approach, 1-amino-1,1-diphosphonate methane (aminoBP) was conjugated to a model protein, albumin. The conjugation was performed by (1) converting the amino group of aminoBP to a thiol group using 2-iminothiolane, (2) derivatizing the albumin amino groups with a thiol-reactive sulfosuccinimidyl-4-(N-maleimidomethyl)-1-cyclohexane carboxylate, and (3) reacting the derivatized albumin with thiolated aminoBP. Typically, 1-4 aminoBP molecules per albumin were obtained. The conjugated albumin exhibited a high affinity to hydroxyapatite that was proportional to the extent of conjugation. The conjugates were shown to exhibit a high affinity to bone matrix in vitro in a serum-containing medium. Once bound to bone matrix, the conjugates were found to desorb more slowly than the unmodified albumin, especially from bone whose organic matrix was removed by ashing. In conclusion, conjugation of bisphosphonates to albumin was shown to impart a high bone affinity to the protein, and such conjugates can be potentially targeted to bone.
A Reliable Gyroscope-Based Gait-Phase Detection Sensor Embedded in a Shoe Insole (2004)

This paper presents results of patient experiments using a new gait-phase detection sensor (GPDS) together with a programmable functional electrical stimulation (FES) system for subjects with a dropped-foot walking dysfunction. The GPDS (sensors and processing unit) is entirely embedded in a shoe insole and detects in real time four phases (events) during the gait cycle: stance, heel off, swing, and heel strike. The instrumented GPDS insole consists of a miniature gyroscope that measures the angular velocity of the foot and three force sensitive resistors that measure the force load on the shoe insole at the heel and the metatarsal bones. The extracted gait-phase signal is transmitted from the embedded microcontroller to the electrical stimulator and used in a finite state control scheme to time the electrical stimulation sequences. The electrical stimulations induce muscle contractions in the paralyzed muscles leading to a more physiological motion of the affected leg. The experimental results of the quantitative motion analysis during walking of the affected and nonaffected sides showed that the use of the combined insole and FES system led to a significant improvement in the gait-kinematics of the affected leg. This combined sensor and stimulation system has the potential to serve as a walking aid for rehabilitation training or permanent use in a wide range of gait disabilities after brain stroke, spinal-cord injury, or neurological diseases.