gebhart/patrepeval huggingface dataset:
Regulation of the Bacillus subtilis alsS, alsD, and alsR genes involved in post-exponential-phase production of acetoin (1993)

Acetoin is a major extracellular product of Bacillus subtilis grown on glucose and other fermentable carbon sources. The enzymes responsible for the formation of acetoin, acetolactate synthase, and acetolactate decarboxylase are synthesized in detectable amounts only in cells that have reached stationary phase. We have cloned and sequenced the genes encoding these enzymes, alsS and alsD, as well as a gene, alsR, that regulates their expression. alsS and alsD appear to compose a single operon, while alsR is transcribed divergently from the alsSD operon. AlsR shows significant homology to the LysR family of bacterial activator proteins, and when alsR is disrupted the alsSD operon is not expressed. Transcriptional fusions to alsS and alsR revealed that AlsR is required for the transcription of the alsSD operon, which increases during stationary phase. Two mutations that cause increased expression of the alsSD operon have been isolated, cloned, and sequenced. They each change an amino acid in the AlsR protein.
Efficient genome editing in plants using a CRISPR/Cas system (2013)

In the past few years, the development of sequence-specific DNA nucleases has progressed rapidly and such nucleases have shown their power in generating efficient targeted mutagenesis and other genome editing applications. For zinc finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs), an engineered array of sequence-specific DNA binding domains are fused with the DNA nuclease Fok1. These nucleases have been successful in genome modifications by generating double strand breaks (DSBs), which are then repaired through non-homologous end joining (NHEJ) or homologous recombination (HR) in different species, including mouse, tobacco and rice. Recently, another breakthrough technology for genome editing, the CRISPR/Cas system, was developed. CRISPR (clustered regulatory interspaced short palindromic repeats) loci are variable short spacers separated by short repeats, which are transcribed into non-coding RNAs. The non-coding RNAs form a functional complex with CRISPR-associated (Cas) proteins and guide the complex to cleave complementary invading DNA. After the initial development of a programmable CRISPR/Cas system, it has been rapidly applied to achieve efficient genome editing in human cell lines, zebrafish and mouse. However, there is still no successful application in plants reported.
The Vulnerable Carotid Artery Plaque (2005)

A multimodal assessment of plaque vulnerability involving the combination of systemic markers, new imaging methods that target inflammatory and thrombotic components, and the potential of emerging therapies may lead to a new stratification system for atherothrombotic risk and to a better prevention of atherothrombotic stroke.
Meperidine Disposition in Mother, Neonate, and Nonpregnant Females (1981)

KUHNERT, B. R.; KUHNERT, P. M.; PROCHASKA, A. L.; SOKOL, R. J.; Virtue, Robert W. M.D. Author Information
Part II 新媒体联盟地平线报告(2013基础教育版) (2013)

一、概述国际社会关注的系列出版物《新媒体联盟地平线报告》和区域性《新媒体联盟技术展望》是新媒体联盟主持的地平线项目的组成部分。地平线项目始于2002年,主要目的在于预测和描述未来5年全球范围内可能对教育产生重大影响
Preliminary studies and potential applications of localized surface plasmon resonance spectroscopy in medical diagnostics (2004)

Miniature optical sensors that specifically identify low concentrations of environmental and biological substances are in high demand. Currently, there is no optical sensor that provides identification of the aforementioned species without amplification techniques at naturally occurring concentrations. Recently, it has been demonstrated that triangular silver nanoparticles have remarkable optical properties and that their enhanced sensitivity to their nanoenvironment has been used to develop a new class of optical sensors using localized surface plasmon resonance spectroscopy. The examination of both model and nonmodel biological assays using localized surface plasmon resonance spectroscopy will be presented in this review. It will be demonstrated that the use of a localized surface plasmon resonance nanosensor rivals the sensitivity and selectivity of, and provides a low-cost alternative to, commercially available sensors.
Surveying a local fitness landscape of a protein with epistatic sites for the study of directed evolution (2002)

We present a method for analysis of a fitness landscape of a biopolymer with significantly epistatic sites. The analysis is based on a quasi-additive fitness model. The fitness model is constructed with additive terms conducted by "site-fitness" and epistatic terms conducted by "pair-fitness," where the site-fitness is a fitness contribution from an independent residue and the pair-fitness is a fitness contribution from a pair of epistatic residues. As a case study, we analyzed the sequence-fitness data for 45 clones of thermostable prolyl endopeptidase mutants. They were generated by a mutation scrambling method, which can accumulate advantageous mutations. The fitness contributions from 14 single-point mutations including E67Q and Q656R were identified by the analysis. As a result, we found that the fitness model with a significant epistatic term by a pair of the 67th site and 656th site was in good agreement with the experimental data and that the explored landscape in the binary 14-dimensional sequence space is still a mountainous landscape with twin peaks. The validity was supported by the analysis of mutant fitness distributions derived from another mutation scrambling experiment and by (3D) structural data.
Soft-Tissue Injury Associated With Closed Fractures: Evaluation and Management (2003)

Determination of the severity of injury to the soft tissues is an important component of patient assessment and affects management of closed fractures. The response of soft tissue to blunt injury involves microvascular and inflammatory processes that produce localized tissue hypoxia and acidosis. Incisions placed through such compromised tissue can lead to wound breakdown and deep infection. Therefore, recognizing the signs of soft-tissue injury is the foundation for successful management of closed fractures. Many treatment options, including splinting, cryotherapy, compression, and delayed surgery, help limit further soft-tissue injury and facilitate its rapid recovery before surgical intervention. Emerging surgical techniques based on improved management have resulted in decreased rates of soft-tissue complications.
Using fast weights to improve persistent contrastive divergence (2009)

The most commonly used learning algorithm for restricted Boltzmann machines is contrastive divergence which starts a Markov chain at a data point and runs the chain for only a few iterations to get a cheap, low variance estimate of the sufficient statistics under the model. Tieleman (2008) showed that better learning can be achieved by estimating the model's statistics using a small set of persistent "fantasy particles" that are not reinitialized to data points after each weight update. With sufficiently small weight updates, the fantasy particles represent the equilibrium distribution accurately but to explain why the method works with much larger weight updates it is necessary to consider the interaction between the weight updates and the Markov chain. We show that the weight updates force the Markov chain to mix fast, and using this insight we develop an even faster mixing chain that uses an auxiliary set of "fast weights" to implement a temporary overlay on the energy landscape. The fast weights learn rapidly but also decay rapidly and do not contribute to the normal energy landscape that defines the model.
Detection of neonates with mild congenital hypothyroidism (primary) or isolated hyperthyrotropinemia: an increasingly common management dilemma (2014)

Anywhere from 10% to 40% of neonates detected by newborn screening programs have mild congenital hypothyroidism (thyroid-stimulating hormone [TSH] 6 to 20 mU/l with borderline low free T4) or isolated hyperthyrotropinemia. The increasing frequency of such cases appears to be chiefly the result of lowering screening TSH cutoffs. In some cases, the etiology is a mild form of dysgenesis or dyshormonogenesis; most cases, however, on imaging have gland in situ of unexplained etiology. Re-evaluation after age 3 years shows some with transient hypothyroidism, a minority with permanent hypothyroidism, while the majority have persistent, mild TSH elevation and normal free T4. There is limited data on neurodevelopmental outcome to guide management. In cases where the TSH is trending down and free T4 is normal, we recommend re-checking serum TSH and free T4 at weekly intervals. If serum TSH does not normalize by 4 weeks of age, we recommend treatment, with re-evaluation after age 2-3 years.
Essential function of Wnt-4 in mammary gland development downstream of progesterone signaling (2000)

Female reproductive hormones control mammary gland morphogenesis. In the absence of the progesterone receptor (PR) from the mammary epithelium, ductal side-branching fails to occur. We can overcome this defect by ectopic expression of the protooncogene Wnt-1. Transplantation of mammary epithelia from Wnt-4(-)/(-) mice shows that Wnt-4 has an essential role in side-branching early in pregnancy. PR and Wnt-4 mRNAs colocalize to the luminal compartment of the ductal epithelium. Progesterone induces Wnt-4 in mammary epithelial cells and is required for increased Wnt-4 expression during pregnancy. Thus, Wnt signaling is essential in mediating progesterone function during mammary gland morphogenesis.
Human Peptidoglycan Recognition Protein-L Is an N-Acetylmuramoyl-L-alanine Amidase (2003)

Peptidoglycan recognition proteins (PGRPs) are pattern recognition molecules coded by up to 13 genes in insects and 4 genes in mammals. In insects PGRPs activate antimicrobial pathways in the hemolymph and cells, or are peptidoglycan (PGN)-lytic amidases. In mammals one PGRP is an antibacterial neutrophil protein. We report that human PGRP-L is a Zn2+-dependent N-acetylmuramoyl-l-alanine amidase (EC 3.5.1.28), an enzyme that hydrolyzes the amide bond between MurNAc and l-Ala of bacterial PGN. The minimum PGN fragment hydrolyzed by PGRP-L is MurNAc-tripeptide. PGRP-L has no direct bacteriolytic activity. The other members of the human PGRP family, PGRP-Ialpha, PGRP-Ibeta, and PGRP-S, do not have the amidase activity. The C-terminal region of PGRP-L, homologous to bacteriophage and bacterial amidases, is required and sufficient for the amidase activity of PGRP-L, although its activity (in the N-terminal delta1-343 deletion mutant) is reduced. The Zn2+ binding amino acids (conserved in PGRP-L and T7 amidase) and Cys-419 (not conserved in T7 amidase) are required for the amidase activity of PGRP-L, whereas three other amino acids, needed for the activity of T7 amidase, are not required for the activity of PGRP-L. These amino acids, although required, are not sufficient for the amidase activity, because changing them to the "active" configuration does not convert PGRP-S into an active amidase. In conclusion, human PGRP-L is an N-acetylmuramoyl-l-alanine amidase and this function is conserved in prokaryotes, insects, and mammals.
Lipid Sorting and Multivesicular Endosome Biogenesis (2013)

Intracellular organelles, including endosomes, show differences not only in protein but also in lipid composition. It is becoming clear from the work of many laboratories that the mechanisms necessary to achieve such lipid segregation can operate at very different levels, including the membrane biophysical properties, the interactions with other lipids and proteins, and the turnover rates or distribution of metabolic enzymes. In turn, lipids can directly influence the organelle membrane properties by changing biophysical parameters and by recruiting partner effector proteins involved in protein sorting and membrane dynamics. In this review, we will discuss how lipids are sorted in endosomal membranes and how they impact on endosome functions.
Proteomics Analysis of Bladder Cancer Exosomes (2010)

Exosomes are nanometer-sized vesicles, secreted by various cell types, present in biological fluids that are particularly rich in membrane proteins. Ex vivo analysis of exosomes may provide biomarker discovery platforms and form non-invasive tools for disease diagnosis and monitoring. These vesicles have never before been studied in the context of bladder cancer, a major malignancy of the urological tract. We present the first proteomics analysis of bladder cancer cell exosomes. Using ultracentrifugation on a sucrose cushion, exosomes were highly purified from cultured HT1376 bladder cancer cells and verified as low in contaminants by Western blotting and flow cytometry of exosome-coated beads. Solubilization in a buffer containing SDS and DTT was essential for achieving proteomics analysis using an LC-MALDI-TOF/TOF MS approach. We report 353 high quality identifications with 72 proteins not previously identified by other human exosome proteomics studies. Overrepresentation analysis to compare this data set with previous exosome proteomics studies (using the ExoCarta database) revealed that the proteome was consistent with that of various exosomes with particular overlap with exosomes of carcinoma origin. Interrogating the Gene Ontology database highlighted a strong association of this proteome with carcinoma of bladder and other sites. The data also highlighted how homology among human leukocyte antigen haplotypes may confound MASCOT designation of major histocompatability complex Class I nomenclature, requiring data from PCR-based human leukocyte antigen haplotyping to clarify anomalous identifications. Validation of 18 MS protein identifications (including basigin, galectin-3, trophoblast glycoprotein (5T4), and others) was performed by a combination of Western blotting, flotation on linear sucrose gradients, and flow cytometry, confirming their exosomal expression. Some were confirmed positive on urinary exosomes from a bladder cancer patient. In summary, the exosome proteomics data set presented is of unrivaled quality. The data will aid in the development of urine exosome-based clinical tools for monitoring disease and will inform follow-up studies into varied aspects of exosome manufacture and function.
State-of-the-Art Speech Recognition with Sequence-to-Sequence Models (2018)

Attention-based encoder-decoder architectures such as Listen, Attend, and Spell (LAS), subsume the acoustic, pronunciation and language model components of a traditional automatic speech recognition (ASR) system into a single neural network. In previous work, we have shown that such architectures are comparable to state-of-the-art ASR systems on dictation tasks, but it was not clear if such architectures would be practical for more challenging tasks such as voice search. In this work, we explore a variety of structural and optimization improvements to our LAS model which significantly improve performance. On the structural side, we show that word piece models can be used instead of graphemes. We also introduce a multi-head attention architecture, which offers improvements over the commonly-used single-head attention. On the optimization side, we explore synchronous training, scheduled sampling, label smoothing, and minimum word error rate optimization, which are all shown to improve accuracy. We present results with a unidirectional LSTM encoder for streaming recognition. On a 12, 500 hour voice search task, we find that the proposed changes improve the WER from 9.2% to 5.6%, while the best conventional system achieves 6.7%; on a dictation task our model achieves a WER of 4.1% compared to 5% for the conventional system.
A new technique for analog multiplication (1975)

Describes a new method using emitter current crowding for performing accurate multiplication of analog signals using devices of special geometry but capable of fabrication with a standard bipolar process. A narrow region of current injection-a carrier domain-can be positioned on an emitter by one electrical input and controlled in magnitude by a second input. The resistive epi layer resolves this current into a differential output proportional to the product of the inputs. A key advantage of these multipliers is their low noise. The basic principle can be applied to many other nonlinear operations. A two-quadrant and a four-quadrant multiplier are described.
Identification of Human Ether-à-go-go Related Gene Modulators by Three Screening Platforms in an Academic Drug-Discovery Setting (2010)

The human Ether-à-go-go related gene (hERG) potassium channel is responsible for the rapid delayed rectifier potassium current that plays a critical role in the repolarization of cardiomyocytes during the cardiac action potential. In humans, inhibition of hERG by drugs can prolong the electrocardiographic QT interval, which, in rare instance, leads to ventricular arrhythmia and sudden cardiac death. As such, several medications that block hERG channels in vitro have been withdrawn from the market due to QT prolongation and arrhythmias. The current FDA guidelines recommend that drug candidates destined for human use be evaluated for potential hERG activity ( www.fda.gov/downloads/Drugs/GuidanceComplianceRegulatoryInformation/Guidances/ucm074963.pdf ). Here, we employed automated planar patch clamp (APPC), high-throughput fluorescent Tl(+) flux, and moderate-throughput [³H]dofetilide competition binding assays to characterize a panel of 49 drugs for their activities at the hERG channel. Notably, we used the same HEK293-hERG cell line for all assays, facilitating comparisons of hERG potencies across screening platforms. In general, hERG inhibitors were most potent in APPC assays, intermediate potent in [³H]dofetilide binding assays, and least potent in Tl(+) flux assays. Binding affinity constants (pK(i) values) and Tl(+) flux potencies (pEC₅₀ values) correlated well with APPC pEC₅₀ values. Further, the inhibitory potencies of many known hERG inhibitors in APPC matched literature values from manual and/or automated patch clamp systems. We also developed a novel fluorescent Tl(+) flux assays to measure the effects of drugs that modulate hERG trafficking and surface expression.
Enhanced Bone Regeneration Using Porcine Small Intestinal Submucosa (1999)

Small intestinal submucosa (SIS) is an easily produced material that has been used experimentally for tissue engineering. To evaluate the ability of SIS to facilitate bone growth within a long-bone defect, a segment of the radius was surgically removed in adult, female Sprague-Dawley rats. The defect was either left unfilled or implanted with SIS, demineralized cortical bone (DMCB), or ovalbumin. The defect was evaluated radiographically and histologically after 3, 6, 12, and 24 weeks. Tissue remodeling within the defect was evident by week 3 in SIS- and DMCB-treated rats. Filling was characterized initially by infiltration of mononuclear cells and extracellular material in SIS-implanted rats and multifocal remodeling bone particles and cartilage formation in DMCB-implanted rats. Cartilage was observed as early as 3 weeks and bone as early as 6 weeks in SIS-implanted rats. Filling of the defect arose from multiple foci in DMCB-implanted rats, but was contiguous with and parallel to the ulnar shaft in SIS-implanted rats, suggesting that defect repair by SIS may be conductive rather than inductive. Rats in which the defect was left unfilled demonstrated slow but progressive filling of the defect, characterized by mononuclear cell infiltrates and fibrous extracellular material. In summary, SIS facilitated rapid filling of a long-bone defect. These results suggest that SIS may be useful as a bone repair material.
Lutzomyia longipalpis (Diptera: Psychodidae: Phlebotominae): a review (2003)

Lutzomyia longipalpis is the most important vector of AmericanVisceral Leishmaniasis (AVL) due to Leishmania chagasi in the New World. Despite its importance, AVL, a disease primarily of rural areas, has increased its prevalence and became urbanized in some large cities in Brazil and other countries in Latin America. Although the disease is treatable, other control measures include elimination of infected dogs and the use of insecticides to kill the sand flies. A better understanding of vector biology could also account as one more tool for AVL control. A wide variety of papers about L. longipalpis have been published in the recent past years. This review summarizes our current information of this particular sand fly regarding its importance, biology, morphology, pheromones genetics, saliva, gut physiology and parasite interactions.
Development of an evaporation-based microfluidic sample concentrator (2008)

MicroPlumbers Microsciences LLC, has developed a relatively simple concentrator device based on isothermal evaporation. The device allows for rapid concentration of dissolved or dispersed substances or microorganisms (e.g. bacteria, viruses, proteins, toxins, enzymes, antibodies, etc.) under conditions gentle enough to preserve their specific activity or viability. It is capable of removing of 0.8 ml of water per minute at 37&deg;C, and has dimensions compatible with typical microfluidic devices. The concentrator can be used as a stand-alone device or integrated into various processes and analytical instruments, substantially increasing their sensitivity while decreasing processing time. The evaporative concentrator can find applications in many areas such as biothreat detection, environmental monitoring, forensic medicine, pathogen analysis, and agricultural industrial monitoring. In our presentation, we describe the design, fabrication, and testing of the concentrator. We discuss multiphysics simulations of the heat and mass transport in the device that we used to select the design of the concentrator and the protocol of performance testing. We present the results of experiments evaluating water removal performance.
InP-based balanced photodiodes heterogeneously integrated on SOI nano-waveguides (2016)

We demonstrate modified uni-traveling carrier balanced photodiodes (PDs) with top p-contact heterogeneously integrated on silicon-on-insulator (SOI) nano-waveguides. The photodiodes have low dark current and high bandwidth of 200 nA and 20 GHz, respectively. The common mode rejection ratio (CMRR) is 20 dB. The RF output power at 15 GHz of a single photodiode reaches 8.5 dBm at 25 mA and 3 V reverse bias.