gebhart/patrepeval huggingface dataset:
Isolation and Characterization of Satellite Cells from Rat Head Branchiomeric Muscles (2015)

Fibrosis and defective muscle regeneration can hamper the functional recovery of the soft palate muscles after cleft palate repair. This causes persistent problems in speech, swallowing, and sucking. In vitro culture systems that allow the study of satellite cells (myogenic stem cells) from head muscles are crucial to develop new therapies based on tissue engineering to promote muscle regeneration after surgery. These systems will offer new perspectives for the treatment of cleft palate patients. A protocol for the isolation, culture and differentiation of satellite cells from head muscles is presented. The isolation is based on enzymatic digestion and trituration to release the satellite cells. In addition, this protocol comprises an innovative method using extracellular matrix gel coatings of millimeter size, which requires only low numbers of satellite cells for differentiation assays.
Web-scale named entity recognition (2008)

Automatic recognition of named entities such as people, places, organizations, books, and movies across the entire web presents a number of challenges, both of scale and scope. Data for training general named entity recognizers is difficult to come by, and efficient machine learning methods are required once we have found hundreds of millions of labeled observations. We present an implemented system that addresses these issues, including a method for automatically generating training data, and a multi-class online classification training method that learns to recognize not only high level categories such as place and person, but also more fine-grained categories such as soccer players, birds, and universities. The resulting system gives precision and recall performance comparable to that obtained for more limited entity types in much more structured domains such as company recognition in newswire, even though web documents often lack consistent capitalization and grammatical sentence construction.
α2-Heremans-Schmid Glycoprotein/ Fetuin-A Is Associated With Insulin Resistance and Fat Accumulation in the Liver in Humans (2006)

We found that high AHSG plasma levels are associated with insulin resistance in humans. Moreover, AHSG plasma levels are elevated in subjects with fat accumulation in the liver. This is consistent with a potential role of AHSG as a link between fatty liver and insulin resistance.
Modeling the Vulnerability Discovery Process (2006)

Security vulnerabilities in servers and operating systems are software defects that represent great risks. Both software developers and users are struggling to contain the risk posed by these vulnerabilities. The vulnerabilities are discovered by both developers and external testers throughout the life-span of a software system. A few models for the vulnerability discovery process have just been published recently. Such models will allow effective resource allocation for patch development and are also needed for evaluating the risk of vulnerability exploitation. Here we examine these models for the vulnerability discovery process. The models are examined both analytically and using actual data on vulnerabilities discovered in three widely-used systems. The applicability of the proposed models and significance of the parameters involved are discussed. The limitations of the proposed models are examined and major research challenges are identified
Dynamic timing analysis considering power supply noise effects (2002)

Power supply noise can significantly impact the performance of deep submicron designs. Existing timing analysis techniques cannot capture the effects of power supply noise on the signal/cell delays. This is because these delay effects are highly input pattern dependent. Therefore, the predicted circuit performance might not reflect the worst-case circuit delay. In this paper, we propose a dynamic timing analysis technique that can take into account the impact of the power supply noise on the signal/cell propagation delays. Our technique is based on considering the input patterns that produce the worst-case power supply noise effects on the propagation delays of the longest true paths in the circuit. Our experimental results show that the circuit delay predicted by our dynamic timing analysis method is significantly longer than the delay predicted suing traditional timing analysis tools.
A model of queries for object-oriented databases (1989)

One major source of confusion, and consequent c&icisms, about object-oriented databases has been the lack of a comprehensive model of queries. Although there is a reasonable degree of agreement about an object-oriented data model, few operational systems support a query model for object-oriented databases. In this paper, we present a rather comprehensive query model which is consistent with object-oriented concepts embodied in the object-oriented data model. The model takes into account the semantics of the class hierarchy and nested objects, and as such is inherently richer than the relational or nested relational model of queries. A significant subset of the model has been cast into a query language which is supported in the ORION object-oriented database system.
Translation camera on mobile phone (2003)

In this paper, we report a mobile application, which translates Japanese texts in a scene into English. The application is designed to run on a mobile phone with a camera. It recognizes Japanese characters sensed by an onboard camera of a mobile phone and translates them into English.
A new methodology for gray-scale character segmentation and recognition (1996)

Generally speaking, through the binarization of gray-scale images, useful information for the segmentation of touched or overlapped characters may be lost in many cases. If we analyze gray-scale images, however, specific topographic features and the variation of intensities can be observed in the character boundaries. In this paper, we propose a new methodology for character segmentation and recognition which makes the best use of the characteristics of gray-scale images. In the proposed methodology, the character segmentation regions are determined by using projection profiles and topographic features extracted from the gray-scale images. Then a nonlinear character segmentation path in each character segmentation region is found by using multi-stage graph search algorithm. Finally, in order to confirm the nonlinear character segmentation paths and recognition results, a recognition-based segmentation method is adopted. Through the experiments with various kinds of printed documents, it is convinced that the proposed methodology is very effective for the segmentation and recognition of touched and overlapped characters.
Nuclear-Cytoplasmic Interaction and Development of Goat Embryos Reconstructed by Nuclear Transplantation: Production of Goats by Serially Cloning Embryos1 (1998)

The time of pronuclear formation of in vivo-matured oocytes was examined. Maturation-promoting factor (MPF) activity in enucleated and electrically activated oocytes was checked by assessment of nuclear envelope breakdown (NEBD) of fused blastomeres. The effect of stage of the cell cycle of donor cells and recipient oocytes on DNA synthesis and development of reconstructed embryos was studied. MPF activity declined rapidly to approximately 63.2% at 1 h, to 9.7% at 5 h, and to the level at which NEBD cannot occur at 7 h postactivation. All blastomeres that were fused at the time of recipient cytoplasm activation underwent NEBD and subsequent DNA synthesis. However, when blastomeres were fused to enucleated oocytes at 7 h postactivation, no NEBD was observed; DNA was replicated in nuclei at the G1/S border, but in G2 nuclei no DNA replication was observed. The proportion of development to blastocysts of reconstructed goat embryos increased with the decline in MPF activity in fused recipient cytoplasm when reconstruction took place at 0-6 h postactivation of enucleated oocytes. Generations 1, 2, 3, 4, 5, and 6 of cloned goat embryos were produced by a combination of nuclear transplantation and in vitro techniques. After transfer to recipients, 45 kids were obtained, including three pairs of monozygotic twins, three series of monozygotic triplets, two series of monozygotic quadruplets, three series of monozygotic quintuplets, and one series of monozygotic heptaplets. The present study indicates that normal DNA replication of goat blastomere nuclei can be accomplished in enucleated oocytes when MPF activity is low, regardless of the stage of the cell cycle of donor nuclei; induction of NEBD and prematuration chromosome condensation is not essential for further development of reconstructed goat embryos.
Regulation of transcription of cellulases- and hemicellulases-encoding genes in Aspergillus niger and Hypocrea jecorina (Trichoderma reesei) (2008)

The filamentous fungi Aspergillus niger and Hypocrea jecorina (Trichoderma reesei) have been the subject of many studies investigating the mechanism of transcriptional regulation of hemicellulase- and cellulase-encoding genes. The transcriptional regulator XlnR that was initially identified in A. niger as the transcriptional regulator of xylanase-encoding genes controls the transcription of about 20-30 genes encoding hemicellulases and cellulases. The orthologous xyr1 (xylanase regulator 1-encoding) gene product of H. jecorina has a similar function as XlnR, although at points, the mechanisms seems to be different. Specifically in H. jecorina, the interaction of Xyr1 and the co-regulators Ace1 and Ace2 in the regulation of transcription of xylanases and cellulases has been studied. This paper describes the similarities and differences in the transcriptional regulation of expression of hemicellulases and cellulases in A. niger and H. jecorina.
PointCNN: convolution on Χ -transformed points (2018)

We present a simple and general framework for feature learning from point clouds. The key to the success of CNNs is the convolution operator that is capable of leveraging spatially-local correlation in data represented densely in grids (e.g. images). However, point clouds are irregular and unordered, thus directly convolving kernels against features associated with the points will result in desertion of shape information and variance to point ordering. To address these problems, we propose to learn an Χ-transformation from the input points to simultaneously promote two causes: the first is the weighting of the input features associated with the points, and the second is the permutation of the points into a latent and potentially canonical order. Element-wise product and sum operations of the typical convolution operator are subsequently applied on the Χ-transformed features. The proposed method is a generalization of typical CNNs to feature learning from point clouds, thus we call it PointCNN. Experiments show that PointCNN achieves on par or better performance than state-of-the-art methods on multiple challenging benchmark datasets and tasks.
Identification of a Class of HCV Inhibitors Directed Against the Nonstructural Protein NS4B (2010)

New classes of drugs are needed to combat hepatitis C virus (HCV), an important worldwide cause of liver disease. We describe an activity of a key domain, an amphipathic helix we termed 4BAH2, within a specific HCV nonstructural protein, NS4B. In addition to its proposed role in viral replication, we validate 4BAH2 as essential for HCV genome replication and identify first-generation small-molecule inhibitors of 4BAH2 that specifically prevent HCV replication within cells. Mechanistic studies reveal that the inhibitors target 4BAH2 function by preventing either 4BAH2 oligomerization or 4BAH2 membrane association. 4BAH2 inhibitors represent an additional class of compounds with potential to effectively treat HCV.
Flow-Join: Adaptive skew handling for distributed joins over high-speed networks (2016)

Modern InfiniBand interconnects offer link speeds of several gigabytes per second and a remote direct memory access (RDMA) paradigm for zero-copy network communication. Both are crucial for parallel database systems to achieve scalable distributed query processing where adding a server to the cluster increases performance. However, the scalability of distributed joins is threatened by unexpected data characteristics: Skew can cause a severe load imbalance such that a single server has to process a much larger part of the input than its fair share and by this slows down the entire distributed query. We introduce Flow-Join, a novel distributed join algorithm that handles attribute value skew with minimal overhead. Flow-Join detects heavy hitters at runtime using small approximate histograms and adapts the redistribution scheme to resolve load imbalances before they impact the join performance. Previous approaches often involve expensive analysis phases, which slow down distributed join processing for non-skewed workloads. This is especially the case for modern high-speed interconnects, which are too fast to hide the extra computation. Other skew handling approaches require detailed statistics, which are often not available or overly inaccurate for intermediate results. In contrast, Flow-Join uses our novel lightweight skew handling scheme to execute at the full network speed of more than 6 GB/s for InfiniBand 4×FDR, joining a skewed input at 11.5 billion tuples/s with 32 servers. This is 6.8× faster than a standard distributed hash join using the same hardware. At the same time, Flow-Join does not compromise the join performance for non-skewed workloads.
Handbook of clinical alcoholism treatment (2003)

Written by leading experts, this handbook is a practical, accessible guide to the diagnosis and treatment of alcoholism. The book reviews the epidemiological, neurobiological, psychological, and sociocultural underpinnings of alcoholism and describes all current diagnostic tools and treatments, including psychotherapeutic, behavioral, and pharmacological interventions and auricular acupuncture. The chapters focus on specific treatment settings, including the emergency department, inpatient alcoholism services, network therapy, primary healthcare settings, rehabilitation programs, the workplace, and the criminal justice system. Other chapters address issues such as prevention, fetal alcohol syndrome, the dually diagnosed patient, alcohol and HIV/AIDS, alcoholism in the elderly, and alcohol problems in women.
Initial human safety and tolerance study of a GABA uptake inhibitor, Cl‐966: Potential role of GABA as a mediator in the pathogenesis of schizophrenia and mania (1990)

Abstract An initial double‐blind, placebo‐controlled safety and tolerance study of single doses of a GABA uptake inhibitor (CI‐966) being developed for the treatment of epilepsy was conducted in healthy volunteers. Drug doses of 1 to 10 mg were well tolerated. A volunteer who received 25 mg of CI‐966 developed transient short‐ and long‐term memory deficits. Both volunteers following administration of 50 mg drug doses presented with a constellation of physical and mental disturbances. Physical abnormalities including tremor, myoclonus, increased muscle rigidity, cogwheeling, and short‐ and long‐term memory impairment of 12–24 hr duration were observed. In addition, striking psychiatric symptoms of many days' duration resembling those seen in patients with mania and schizophrenia were evident. These findings suggest that GABA may modulate memory and dopaminergic pathways responsible for posture and muscle control. In addition, GABA may be a potentially important mediator in the pathogenesis of schizophrenia and mania.
Plasmid Interleukin-23 (IL-23), but Not Plasmid IL-27, Enhances the Protective Efficacy of a DNA Vaccine against<i>Mycobacterium tuberculosis</i>Infection (2005)

Protection against intracellular pathogens such as Mycobacterium tuberculosis requires the development of Th1-like T-cell responses. This in turn is dependent on the pattern of cytokine produced from dendritic cells (DCs) after infection. Three heterodimeric cytokines, interleukin-12 (IL-12), IL-23, and IL-27, as well as IL-18, contribute to the differentiation and expansion of naive CD4(+) T cells. In this study we compared the effects of plasmids expressing both chains of IL-12, IL-23, or IL-27 as adjuvants for DNA immunization against M. tuberculosis infection. The genes encoding p19 and p40 chains of IL-23 or EBI3 and p28 chains of IL-27 were cloned on either side of a self-cleaving peptide from the FMDV2A protein. The secretion of functional cytokines from transfected cells was detected with bioassays. Supernatant from p2AIL-23-transfected cells induced the release of IL-17 from activated lymphocytes, confirming the presence of bioactive IL-23. Further, supernatant from p2AIL-27-transfected cells stimulated a significant increase in the proliferation of peptide-stimulated transgenic CD4(+) T cells. In initial experiments, M. tuberculosis infection of DCs was more potent at inducing IL-12 and IL-23 secretion than infection with the vaccine strain Mycobacterium bovis bacille Calmette-Guérin (BCG), and no significant upregulation of IL-27 was observed. Coimmunization of C57BL/6 mice with DNA expressing M. tuberculosis antigen 85B (Ag85B; DNA85B) and plasmids expressing IL-23 or IL-12 stimulated stronger Ag85B-specific T-cell proliferative and IFN-gamma responses than DNA85B alone, whereas the addition of p2AIL-27 had no effect. Interestingly, DNA85B codelivered with p2AIL-12, but not p2AIL-23, reduced the immunoglobulin G antibody response. Both p2AIL-23 and p2AIL-12, but not p2AIL-27, enhanced the protective efficacy of DNA85B against aerosol M. tuberculosis challenge. Therefore, both p2AIL-23 and p2AIL-12 are valuable as cytokine adjuvants for increasing the protective antituberculosis immunity induced by DNA vaccines.
Application of Genetic Male Sterility to Recurrent Selection Schemes in Soybeans<sup>1</sup> (1973)

Recurrent selection schemes for soybeans [ Glycine max (L.) Merr.] that use a genetic male‐sterile factor to obtain natural crosses are outlined. A basic scheme with three generations per cycle, intermating, advancing, and testing, and modifications of the scheme are discussed. Guidelines for population size and selection intensity are considered. Expected genetic progress is presented for each selection program.
Scheduling Algorithm with Power Allocation for Random Unitary Beamforming (2008)

Random unitary beamforming is one of the schemes that can reduce the amount of feedback information in multiuser diversity techniques with multiple-antenna downlink transmission. In Multiple-Input Multiple-Output (MIMO) systems, throughput performance is greatly improved using AMC (Adaptive Modulation and Coding). Throughput performance is also improved by allocating power among streams appropriately. In random unitary beamforming, the transmitter has only partial channel state information (CSI) of each receiver. Thus, it is difficult for random unitary beamforming to use conventional power allocation methods that assumes that all receivers has full CSI. In this paper, we propose a new scheduling algorithm with power allocation for downlink random unitary beamforming that improves throughput performance without full CSI. We provide numerical results of the proposed scheduling algorithm and compare them to those of the conventional random unitary beamforming scheduling algorithm. We show that random unitary beamforming achieves the best system throughput performance with two transmit antennas. We also show that the proposed algorithm attains higher throughput with the small increase of feedback than the random unitary beamforming scheduling algorithm.
Induction of anti-gp160 cytotoxic T cells cross-reacting with various V3 loop P18 peptides in human immunodeficiency virus type 1 envelope-immunized individuals (1996)

Cytotoxic T lymphocytes (CTL) may be important to prevent cell-to-cell transmission of human immunodeficiency virus type 1 (HIV-1), the agent responsible for AIDS. In this study, we investigated the epitope specificity of CTLs induced in individuals immunized against the virus envelope glycoprotein gp160. The determinant of HIV-1 gp160 for the stimulation of CTL is located in a region of high sequence variability among HIV-1 isolates, the so-called V3 loop P18. Using a panel of P18 peptides, we compared the CTL specificities of cells from two individuals immunized with vaccinia virus recombinants expressing the envelope glycoproteins from two different strains of HIV-1, IIIB and SIMI. For this purpose, CTLs specific for the IIIB P18 peptide (RIQRGPGRAFVTIGK) were compared with CTLs for the site from the SIMI isolate (TLHMGPKRAFYATGD). The results indicate that in contrast to CD8+ CTLs induced by the glycoprotein from strain IIIB, CD8+ CTLs induced by strain SIMI strongly cross-reacted with targets presenting P18 peptides as well as envelope proteins from the divergent MN and RF isolates but failed to cross-react with targets that presented the IIIB peptide. These data have implications for the design of an HIV vaccine.
Transcription factor-based modulation of neural stem cell differentiation using direct protein transduction (2010)

In contrast to conventional gene transfer strategies, the direct introduction of recombinant proteins into cells bypasses the risk of insertional mutagenesis and offers an alternative to genetic intervention. Here, we explore whether protein transduction of the gliogenic transcription factor Nkx2.2 can be used to promote oligodendroglial differentiation of mouse embryonic stem cell (ESC)-derived neural stem cells (NSC). To that end, a recombinant cell-permeant form of Nkx2.2 protein was generated. Exposure of ESC-derived NSC to the recombinant protein and initiation of differentiation resulted in a two-fold increase in the number of oligodendrocytes. Furthermore, Nkx2.2-transduced cells exhibited a more mature oligodendroglial phenotype. Comparative viral gene transfer studies showed that the biological effect of Nkx2.2 protein transduction is comparable to that obtained by lentiviral transduction. The results of this proof-of-concept study depict direct intracellular delivery of transcription factors as alternative modality to control lineage differentiation in NSC cultures without genetic modification.
Translation of Viral mRNA without Active eIF2: The Case of Picornaviruses (2011)

Previous work by several laboratories has established that translation of picornavirus RNA requires active eIF2α for translation in cell free systems or after transfection in culture cells. Strikingly, we have found that encephalomyocarditis virus protein synthesis at late infection times is resistant to inhibitors that induce the phosphorylation of eIF2α whereas translation of encephalomyocarditis virus early during infection is blocked upon inactivation of eIF2α by phosphorylation induced by arsenite. The presence of this compound during the first hour of infection leads to a delay in the appearance of late protein synthesis in encephalomyocarditis virus-infected cells. Depletion of eIF2α also provokes a delay in the kinetics of encephalomyocarditis virus protein synthesis, whereas at late times the levels of viral translation are similar in control or eIF2α-depleted HeLa cells. Immunofluorescence analysis reveals that eIF2α, contrary to eIF4GI, does not colocalize with ribosomes or with encephalomyocarditis virus 3D polymerase. Taken together, these findings support the novel idea that eIF2 is not involved in the translation of encephalomyocarditis virus RNA during late infection. Moreover, other picornaviruses such as foot-and-mouth disease virus, mengovirus and poliovirus do not require active eIF2α when maximal viral translation is taking place. Therefore, translation of picornavirus RNA may exhibit a dual mechanism as regards the participation of eIF2. This factor would be necessary to translate the input genomic RNA, but after viral RNA replication, the mechanism of viral RNA translation switches to one independent of eIF2.