gebhart/patrepeval huggingface dataset:
Ingestion of <i>Lactobacillus</i> strain regulates emotional behavior and central GABA receptor expression in a mouse via the vagus nerve (2011)

There is increasing, but largely indirect, evidence pointing to an effect of commensal gut microbiota on the central nervous system (CNS). However, it is unknown whether lactic acid bacteria such as Lactobacillus rhamnosus could have a direct effect on neurotransmitter receptors in the CNS in normal, healthy animals. GABA is the main CNS inhibitory neurotransmitter and is significantly involved in regulating many physiological and psychological processes. Alterations in central GABA receptor expression are implicated in the pathogenesis of anxiety and depression, which are highly comorbid with functional bowel disorders. In this work, we show that chronic treatment with L. rhamnosus (JB-1) induced region-dependent alterations in GABA(B1b) mRNA in the brain with increases in cortical regions (cingulate and prelimbic) and concomitant reductions in expression in the hippocampus, amygdala, and locus coeruleus, in comparison with control-fed mice. In addition, L. rhamnosus (JB-1) reduced GABA(Aα2) mRNA expression in the prefrontal cortex and amygdala, but increased GABA(Aα2) in the hippocampus. Importantly, L. rhamnosus (JB-1) reduced stress-induced corticosterone and anxiety- and depression-related behavior. Moreover, the neurochemical and behavioral effects were not found in vagotomized mice, identifying the vagus as a major modulatory constitutive communication pathway between the bacteria exposed to the gut and the brain. Together, these findings highlight the important role of bacteria in the bidirectional communication of the gut-brain axis and suggest that certain organisms may prove to be useful therapeutic adjuncts in stress-related disorders such as anxiety and depression.
External human-machine interfaces: Effects of message perspective (2021)

Future automated vehicles may be equipped with external Human-Machine Interfaces (eHMIs). Currently, little is known about the effect of the perspective of the eHMI message on crossing decisions of pedestrians. We performed an experiment to examine the effects of images depicting eHMI messages of different perspectives (egocentric from the pedestrian’s point of view: WALK, DON’T WALK, allocentric: BRAKING, DRIVING, and ambiguous: GO, STOP) on participants’ (N = 103) crossing decisions, response times, and eye movements. Considering that crossing the road can be cognitively demanding, we added a memory task in two-thirds of the trials. The results showed that egocentric messages yielded higher subjective clarity ratings than the other messages as well as higher objective clarity scores (i.e., more uniform crossing decisions) and faster response times than the allocentric BRAKING and the ambiguous STOP. When participants were subjected to the memory task, pupil diameter increased, and crossing decisions were reached faster as compared to trials without memory task. Regarding the ambiguous messages, most participants crossed for the GO message and did not cross for the STOP message, which points towards an egocentric perspective taken by the participant. More lengthy text messages (e.g., DON’T WALK) yielded a higher number of saccades but did not cause slower response times. We conclude that pedestrians find egocentric eHMI messages clearer than allocentric ones, and take an egocentric perspective if the message is ambiguous. Our results may have important implications, as the consensus among eHMI researchers appears to be that egocentric text-based eHMIs should not be used in traffic.
The Institution-Based Prospective Inception Cohort Study: Design, Implementation, and Quality Assurance in Pediatric Thrombosis and Stroke Research (2012)

The development of well-designed cohort studies in rare diseases can lead to the discovery of new risk factors and prognostic markers, enhance understanding of natural history and outcomes, and provide preliminary data for randomized controlled trials of treatment strategies. Designing a robust cohort requires substantial upfront design and planning. Ideally, a cohort study of diseased individuals follows patients prospectively from the time of diagnosis (i.e., from the disease's inception). The objective of this article is to discuss the design and implementation of an institution-based prospective inception cohort study, with applied examples in pediatric stroke and thrombosis. Furthermore, we will discuss the ongoing management and quality assurance mechanisms necessary to optimize such a study. Although the resources necessary to implement a prospective inception cohort study are large, this approach can provide critical observational evidence on natural history and prognostic factors. Following multicenter validation, its findings can inform the design and execution of much-needed randomized controlled clinical trials.
Knowledge and heuristic-based modeling of laser-scanned trees (2007)

We present a semi-automatic and efficient method for producing full polygonal models of range scanned trees, which are initially represented as sparse point clouds. First, a skeleton of the trunk and main branches of the tree is produced based on the scanned point clouds. Due to the unavoidable incompleteness of the point clouds produced by range scans of trees, steps are taken to synthesize additional branches to produce plausible support for the tree crown. Appropriate dimensions for each branch section are estimated using allometric theory. Using this information, a mesh is produced around the full skeleton. Finally, leaves are positioned, oriented and connected to nearby branches. Our process requires only minimal user interaction, and the full process including scanning and modeling can be completed within minutes.
Tyrosine-Selective Protein Alkylation Using π-Allylpalladium Complexes (2006)

A new protein modification reaction has been developed based on a palladium-catalyzed allylic alkylation of tyrosine residues. This technique employs electrophilic pi-allyl intermediates derived from allylic acetate and carbamate precursors and can be used to modify proteins in aqueous solution at room temperature. To facilitate the detection of modified proteins using SDS-PAGE analysis, a fluorescent allyl acetate was synthesized and coupled to chymotrypsinogen A and bacteriophage MS2. The tyrosine selectivity of the reaction was confirmed through trypsin digest analysis. The utility of the reaction was demonstrated by using taurine-derived carbamates as water solubilizing groups that are cleaved upon protein functionalization. This solubility switching technique was used to install hydrophobic farnesyl and C(17) chains on chymotrypsinogen A in water using little or no cosolvent. Following this, the C(17) alkylated proteins were found to associate with lipid vesicles. In addition to providing a new protein modification strategy targeting an under-utilized amino acid side chain, this method provides convenient access to synthetic lipoproteins.
High Performance Integrated Circuit Design (2012)

The latest techniques for designing robust, high performance integrated circuits in nanoscale technologies Focusing on a new technological paradigm, this practical guide describes the interconnect-centric design methodologies that are now the major focus of nanoscale integrated circuits (ICs). High Performance IntegratedCircuit Design begins by discussing the dominant role of on-chip interconnects and provides an overview of technology scaling. The book goes on to cover data signaling, power management, synchronization, andsubstrate-aware design. Specific design constraints and methodologies unique to each type of interconnect are addressed. This comprehensive volume also explains the design of specialized circuits such as tapered buffers and repeaters for data signaling, voltage regulators for power management, and phase-locked loops for synchronization. This is an invaluable resource for students, researchers, and engineers working in the area of high performance ICs. Coverage includes: Technology scaling Interconnect modeling and extraction Signal propagation and delay analysis Interconnect coupling noise Global signaling Power generation Power distribution networks CAD of power networks Techniques to reduce power supply noise Power dissipation Synchronization theory and tradeoffs Synchronous system characteristics On-chip clock generation and distribution Substrate noise in mixed-signal ICs Techniques to reduce substrate noise
Multiple forms of human renin. Purification and characterization. (1979)

Human renin was purified from a juxtaglomerular cell tumor with a high renin content, 24.2 Goldblatt units/mg of protein. The purification procedure comprised three steps: gel filtration, DEAE-cellulose chromatography, and preparative isoelectric focusing. Five forms of renin amounting to 5.3 mg of enzyme were obtained with isoelectric points of 4.95, 5.10, 5.35, 5.55, and 5.70. They were all glycoproteins. The three major fractions had very similar specific activities, 868, 860, and 809 Goldblatt units/mg of protein. These fractions produced a single band on analytical isoelectric focusing and a single arc on immunoelectrophoresis. On polyacrylamide gel electrophoresis at pH 7.8, each fraction consisted of two renin bands with the same molecular weight, but different net charges. The molecular weight determined by gel filtration and Fergusson plot analysis on polyacrylamide gel was 38,000 to 42,000. The optimum pH determined on N-acetyltetradecapeptide substrate was 6.5, and the Km was 6.8 x 10(-6) M. These parameters were identical with those for standard human kidney renin. Antibodies raised against tumor renin completely inhibited the activity of both tumor and standard renin. Under dissociating conditions (sodium dodecyl sulfate-polyacrylamide gel electrophoresis and gel electrophoresis in the presence of 6 M urea), part of the purified enzyme dissociated into two smaller fragments (Mr = 20,000 and 25,000) containing renin activity.
Two‐Dimensional Electrophoretic Profile of Human Sperm Membrane Proteins (1994)

The purpose of this study was to characterize highly enriched human spermatozoa membrane proteins by two-dimensional electrophoresis and computer image analysis. Sperm membrane proteins were extracted by detergent solubilization from three different preparations: 1) washed semen cells following centrifugation and three wash steps in Ham's F-10 medium (the standard sperm preparation, which is contaminated with seminal immature germ cells, white blood cells, and acellular material), 2) the motile sperm fraction following centrifugation of diluted semen cells through a Percoll density gradient to enrich (> 98%) the viable mature sperm population, and 3) sperm membrane vesicles isolated from Percoll-purified motile mature sperm by nitrogen cavitation followed by differential centrifugation. The two-dimensional gel profiles of extracts of washed semen cells and motile spermatozoa contained more than 600 protein spots between pH 4 and 7 and apparent molecular mass ranging from 7.9 to 93.5 kDa. Only 73% of the major proteins in these two samples matched by computer image analysis. The highly enriched sperm membrane vesicle extract showed a much simpler protein pattern, with only 64 major protein spots, 61 of which could be matched with proteins detected in extracts from purified motile sperm. The isoelectric point and molecular weight coordinates of these major human sperm membrane proteins could serve as a foundation for systematic isolation and further characterization of human sperm antigens for studies of mechanisms of fertilization and the development of contraceptive vaccines.
PCR-Free Quantitative Detection of Genetically Modified Organism from Raw Materials. An Electrochemiluminescence-Based Bio Bar Code Method (2008)

A bio bar code assay based on oligonucleotide-modified gold nanoparticles (Au-NPs) provides a PCR-free method for quantitative detection of nucleic acid targets. However, the current bio bar code assay requires lengthy experimental procedures including the preparation and release of bar code DNA probes from the target-nanoparticle complex and immobilization and hybridization of the probes for quantification. Herein, we report a novel PCR-free electrochemiluminescence (ECL)-based bio bar code assay for the quantitative detection of genetically modified organism (GMO) from raw materials. It consists of tris-(2,2'-bipyridyl) ruthenium (TBR)-labeled bar code DNA, nucleic acid hybridization using Au-NPs and biotin-labeled probes, and selective capture of the hybridization complex by streptavidin-coated paramagnetic beads. The detection of target DNA is realized by direct measurement of ECL emission of TBR. It can quantitatively detect target nucleic acids with high speed and sensitivity. This method can be used to quantitatively detect GMO fragments from real GMO products.
Transcranial magnetic stimulation of the human motor cortex influences the neuronal activity of subthalamic nucleus (2004)

The critical role of the subthalamic nucleus (STN) in the control of movement and parkinsonian symptoms is well established. Research in animals suggests that the cerebral cortex plays an important role in regulating the activity of the STN but this control is not known in humans. The most extensive cortical innervation of the STN originates from motor areas. Here, we used transcranial magnetic stimulation (TMS) during intraoperative single-unit recordings from STN, in six patients with Parkinson's disease (PD) undergoing implantation of deep brain stimulators, to determine whether TMS of the motor cortex (MC) modulates the activity of STN and to investigate in vivo the functional organization of the corticosubthalamic circuit in the human brain. Single-pulse TMS of the MC induced an excitation in 74.9% of neurons investigated. This activation was followed by a long-lasting inhibition of the STN neuronal activity that did not correlate with PD severity. Responsive neurons to TMS of the hand area of motor cortex were located mainly in the lateral and dorsal region of the subthalamus while unresponsive cells had a prevalently medial distribution. This is the first report of TMS-induced modulation of STN neuronal activity in humans. These findings open up new avenues for in vivo studies of corticosubthalamic interactions in human brain and PD.
Hard Zero Shot Learning for Gesture Recognition (2018)

Gesture based systems allow humans to interact with devices and robots in a natural way. Yet, current gesture recognition systems can not recognize the gestures outside a limited lexicon. This opposes the idea of lifelong learning which require systems to adapt to unseen object classes. These issues can be best addressed using Zero Shot Learning (ZSL), a paradigm in machine learning that leverages the semantic information to recognize new classes. ZSL systems developed in the past used hundreds of training examples to detect new classes and assumed that test examples come from unseen classes. This work introduces two complex and more realistic learning problems referred as Hard Zero Shot Learning (HZSL) and Generalized HZSL (G-HZSL) necessary to achieve Life Long Learning. The main objective of these problems is to recognize unseen classes with limited training information and relax the assumption that test instances come from unseen classes. We propose to leverage one shot learning (OSL) techniques coupled with ZSL approaches to address and solve the problem of HZSL for gesture recognition. Further, supervised clustering techniques are used to discriminate seen classes from unseen classes. We assessed and compared the performance of various existing algorithms on HZSL for gestures using two standard datasets: MSRC-12 and CGD2011. For four unseen classes, results show that the marginal accuracy of HZSL-15.2% and G-HZSL-14.39% are comparable to the performance of conventional ZSL. Given that we used only one instance and do not assume that test classes are unseen, the performance of HZSL and G-HZSL models were remarkable.
Gaia: geo-distributed machine learning approaching LAN speeds (2017)

Machine learning (ML) is widely used to derive useful information from large-scale data (such as user activities, pictures, and videos) generated at increasingly rapid rates, all over the world. Unfortunately, it is infeasible to move all this globally-generated data to a centralized data center before running an ML algorithm over it--moving large amounts of raw data over wide-area networks (WANs) can be extremely slow, and is also subject to the constraints of privacy and data sovereignty laws. This motivates the need for a geo-distributed ML system spanning multiple data centers. Unfortunately, communicating over WANs can significantly degrade ML system performance (by as much as 53.7× in our study) because the communication overwhelms the limited WAN bandwidth.

Our goal in this work is to develop a geo-distributed ML system that (1) employs an intelligent communication mechanism over WANs to efficiently utilize the scarce WAN bandwidth, while retaining the accuracy and correctness guarantees of an ML algorithm; and (2) is generic and flexible enough to run a wide range of ML algorithms, without requiring any changes to the algorithms.

To this end, we introduce a new, general geo-distributed ML system, Gaia, that decouples the communication within a data center from the communication between data centers, enabling different communication and consistency models for each. We present a new ML synchronization model, Approximate Synchronous Parallel (ASP), whose key idea is to dynamically eliminate insignificant communication between data centers while still guaranteeing the correctness of ML algorithms. Our experiments on our prototypes of Gaia running across 11 Amazon EC2 global regions and on a cluster that emulates EC2 WAN bandwidth show that Gaia provides 1.8-53.5× speedup over two state-of-the-art distributed ML systems, and is within 0.94-1.40× of the speed of running the same ML algorithm on machines on a local area network (LAN).
Vibration feature extraction techniques for fault diagnosis of rotating machinery : a literature survey (2003)

Acidity of products resulting from the reaction of flue gas components emitted from a coal-fired power plant with water contained in a vapor plume from a wet cooling tower was analyzed in a close vicinity of a power plant (710 m from the stack and 315 m from the cooling tower). Samples of this mixture were collected using a precipitation funnel where components of the mixed plumes were discharged from the atmosphere with the rainfall. To identify situations when the precipitation occurred at the same time as the wind directed the mixed vapor and flue gas plumes above the precipitation funnel, an ultrasound anemometer designed for 3D measurements of the wind field located near the funnel was used. Precipitation samples of extremely high acidity were identified - about 5% of samples collected during 12 months showed the acidity below pH=3 and the lowest recorded pH was 1.4. During the measurement period the value of pH characterizing the background acidity of the precipitation was about 6. The main outcome of this study was to demonstrate a very high, and so far completely underestimated, potential of occurrence of episodes of extremely acid depositions in the immediate vicinity of a coal-fired power plant.
The First General Method for Palladium-Catalyzed Negishi Cross-Coupling of Aryl and Vinyl Chlorides:  Use of Commercially Available Pd(P(<i>t</i>-Bu)<sub>3</sub>)<sub>2</sub>as a Catalyst (2001)

With a single protocol, commercially available Pd(P(t-Bu)(3))(2) can effect the Negishi cross-coupling of a wide range of aryl and vinyl chlorides with aryl- and alkylzinc reagents. The process tolerates nitro groups, and it efficiently generates sterically hindered biaryls. In addition, a high turnover number (>3000) can be achieved.
Genetic polymorphism and prostate cancer aggressiveness: A case‐only study of 1,536 GWAS and candidate SNPs in African‐Americans and European‐Americans (2012)

Some replicated GWAS susceptibility SNPs may play a role in CaP aggressiveness. However, like susceptibility, these associations are not consistent between racial groups.
Selection of Optimal Programming Contacts Based on Local Field Potential Recordings From Subthalamic Nucleus in Patients With Parkinson's Disease (2010)

Postoperative subband analysis of LFP recordings in beta and gamma frequency ranges may be used to select optimal electrode contacts. These results indicate that LFP recordings from implanted DBS electrodes can provide important clues to guide the optimization of DBS therapy in individual patients.
Asymmetric Division of <i>Drosophila</i> Male Germline Stem Cell Shows Asymmetric Histone Distribution (2012)

Stem cells can self-renew and generate differentiating daughter cells. It is not known whether these cells maintain their epigenetic information during asymmetric division. Using a dual-color method to differentially label "old" versus "new" histones in Drosophila male germline stem cells (GSCs), we show that preexisting canonical H3, but not variant H3.3, histones are selectively segregated to the GSC, whereas newly synthesized histones incorporated during DNA replication are enriched in the differentiating daughter cell. The asymmetric histone distribution occurs in GSCs but not in symmetrically dividing progenitor cells. Furthermore, if GSCs are genetically manipulated to divide symmetrically, this asymmetric mode is lost. This work suggests that stem cells retain preexisting canonical histones during asymmetric cell divisions, probably as a mechanism to maintain their unique molecular properties.
Estrogen Influences Cocaine-Induced Blood Oxygen Level-Dependent Signal Changes in Female Rats (2005)

We investigated the effect of estrogen on cocaine-induced brain activity using blood oxygen level-dependent (BOLD) magnetic resonance imaging. Ovariectomized (Ovx) rats without estrogen and Ovx rats with estrogen (Ovx+E) were given a single saline or cocaine injection (15 mg/kg, i.p.) for 5 d. After 7 d of withdrawal from injections, rats were challenged with cocaine during functional imaging. Acute cocaine administration produced positive BOLD activation in the prefrontal cortex, nucleus accumbens, striatum, ventral tegmental area, and hippocampus, among other brain regions. Positive BOLD signal changes were lower in Ovx+E than in Ovx rats. With repeated cocaine administration, Ovx+E rats showed enhanced BOLD signal changes in the nucleus accumbens, ventral tegmental area, and hippocampus compared with acutely treated animals. Our results indicate that estrogen influences the effects of acute and repeated cocaine administration on BOLD signal changes. The data suggest that in females with estrogen, cocaine-induced neuronal activity is enhanced after repeated cocaine administration. It is possible that the actions of estrogen within the aforementioned brain regions potentiate the behavioral response to cocaine observed in female rats.
The design of a redundant array of independent net-storages for improved confidentiality in cloud computing (2012)

This article describes how a Redundant Array of Independent Net-storages (RAIN) can be deployed for confidentiality control in Cloud Computing. The RAIN approach splits data into segments and distributes segments between multiple storage providers; by keeping the distribution of segments and the relationships between the distributed segments private, the original data cannot be re-assembled by an observer. As long as each segment is small enough, an individual segment discloses no meaningful information to others, and hence RAIN is able to ensure the confidentiality of data stored in the clouds. We describe the inter-cloud communication protocol, and present a formal model, security analysis, and simulation results.