gebhart/patrepeval huggingface dataset:
Critical Structural Elements of the VP16 Transcriptional Activation Domain (1991)

Virion protein 16 (VP16) of herpes simplex virus type 1 contains an acidic transcriptional activation domain. Missense mutations within this domain have provided insights into the structural elements critical for its function. Net negative charge contributed to, but was not sufficient for, transcriptional activation by VP16. A putative amphipathic alpha helix did not appear to be an important structural component of the activation domain. A phenylalanine residue at position 442 was exquisitely sensitive to mutation. Transcriptional activators of several classes contain hydrophobic amino acids arranged in patterns resembling that of VP16. Therefore, the mechanism of transcriptional activation by VP16 and other proteins may involve both ionic and specific hydrophobic interactions with target molecules.
Heterogeneous die stacking of SRAM row cache and 3-D DRAM: An empirical design evaluation (2011)

As DRAM scaling becomes more challenging and its energy efficiency receives a growing concern for data center operation, an alternative approach- stacking DRAM die with thru-silicon vias (TSV) using 3-D integration technology is being undertaken by industry to address these looming issues. Furthermore, 3-D technology also enables heterogeneous die stacking within one DRAM package. In this paper, we study how to design such a heterogeneous DRAM chip for improving both performance and energy efficiency, in particular, we propose a novel floorplan and several architectural techniques to fully exploit the benefits of 3-D die stacking technology when integrating an SRAM row cache into a DRAM chip. Our multi-core simulation results show that, by tightly integrating a small row cache with its corresponding DRAM array, we can improve performance by 30% while saving dynamic energy by 31% for memory intensive applications.
Overcoming the Phage Replication Threshold: a Mathematical Model with Implications for Phage Therapy (2002)

Prior observations of phage-host systems in vitro have led to the conclusion that susceptible host cell populations must reach a critical density before phage replication can occur. Such a replication threshold density would have broad implications for the therapeutic use of phage. In this report, we demonstrate experimentally that no such replication threshold exists and explain the previous data used to support the existence of the threshold in terms of a classical model of the kinetics of colloidal particle interactions in solution. This result leads us to conclude that the frequently used measure of multiplicity of infection (MOI), computed as the ratio of the number of phage to the number of cells, is generally inappropriate for situations in which cell concentrations are less than 10(7)/ml. In its place, we propose an alternative measure, MOI(actual), that takes into account the cell concentration and adsorption time. Properties of this function are elucidated that explain the demonstrated usefulness of MOI at high cell densities, as well as some unexpected consequences at low concentrations. In addition, the concept of MOI(actual) allows us to write simple formulas for computing practical quantities, such as the number of phage sufficient to infect 99.99% of host cells at arbitrary concentrations.
Optimization of copper pillar bump design for fine pitch flip-chip packages (2009)

In this paper we present new approaches in the development of flip chip technology. We assess the challenges presented by micro bump interconnection. In order to study that we have evaluated different bump designs of stagger 50 um pitch using different flip-chip packages methods Mold Under-filling (MUF) & Capillary Under-filling (CUF). (Figure 1) Finally this paper will conclude by identifying the most robust Cu pillar bump design for fine pitch FCCSP devices.
Negative Feedback Regulation of TGF-β Signaling by the SnoN Oncoprotein (1999)

Smad proteins mediate transforming growth factor-beta (TGF-beta) signaling to regulate cell growth and differentiation. The SnoN oncoprotein was found to interact with Smad2 and Smad4 and to repress their abilities to activate transcription through recruitment of the transcriptional corepressor N-CoR. Immediately after TGF-beta stimulation, SnoN is rapidly degraded by the nuclear accumulation of Smad3, allowing the activation of TGF-beta target genes. By 2 hours, TGF-beta induces a marked increase in SnoN expression, resulting in termination of Smad-mediated transactivation. Thus, SnoN maintains the repressed state of TGF-beta-responsive genes in the absence of ligand and participates in negative feedback regulation of TGF-beta signaling.
The FDA-NIMH-MATRICS Guidelines for Clinical Trial Design of Cognitive-Enhancing Drugs: What Do We Know 5 Years Later? (2010)

The Food and Drug Administration (FDA)-National Institute of Mental Health (NIMH)-Measurement and Treatment Research to Improve Cognition in Schizophrenia (MATRICS) clinical trial guidelines for cognitive-enhancing drugs in schizophrenia and the MATRICS Consensus Cognitive Battery (MCCB) were designed to facilitate novel compound development in the treatment of cognitive impairments. Several studies have recently utilized the FDA-NIMH-MATRICS guidelines and MCCB and allow an evaluation of the feasibility of guideline implementation and MCCB performance. In light of the study results, we would recommend the following inclusion criteria revisions-(1) clinical status and symptom inclusion criteria: maximum allowed score for hallucinations and delusions should be increased from moderate to moderately severe and the negative symptom criterion should be dropped in phase 2 studies; (2) antipsychotic medication inclusion criteria: first-generation antipsychotics should be allowed, but only in the context of no concomitant anticholinergic agents and minimal extrapyramidal symptoms, and antipsychotic polypharmacy should be allowed in the absence of pertinent pharmacokinetic or pharmacodynamic considerations; and (3) people who use illicit substances should not be allowed in phase 1B or 2A proof-of-concept studies but may be included in phase 2B and 3 studies in which proof of effectiveness and generalizability of results become more important goals. These revisions are recommended to enhance recruitment while maintaining sufficient methodological rigor to ensure the validity of study results. The MCCB has been shown to have excellent psychometric characteristics, including reliability for multisite clinical trials, clinical relevance for real-world functioning, and possible sensitivity to behavioral treatment, and should continue to serve as the standard outcome measure for cognitive enhancement studies in schizophrenia.
Epidemiology of Community-Acquired Clostridium difficile-Associated Diarrhea (1994)

The epidemiology of clinically recognized community-acquired Clostridium difficile-associated diarrhea was assessed in a retrospective cohort study of members of a health maintenance organization (HMO). Potential cases were identified through positive toxin assay results and confirmed by review of automated full-text medical records. Of 51 cases identified (7.7 per 100,000 person-years), 42 (82%) were diagnosed and treated exclusively in the ambulatory care setting; 33 cases occurred within 42 days after 494,491 exposures to antibiotics dispensed by an HMO pharmacy. Antibiotic-specific attack rates varied from 0 to 2040 cases per 100,000 exposures. Increased age was associated with C. difficile-associated diarrhea (P < .001). Age-adjusted antibiotic-specific attack rates were at least 10-fold higher (P < .05) for nitrofurantoin, cefuroxime, cephalexin plus dicloxacillin, ampicillin/clavulanate plus cefaclor, and ampicillin/clavulanate plus cefuroxime than for ampicillin or amoxicillin; several other antibiotics were associated with similar but not significantly increased risks.
RNA interference in protozoan parasites (2004)

RNA interference or RNAi is defined as the mechanism through which gene-specific, double-stranded RNA (dsRNA) triggers degradation of homologous transcripts. Besides providing an invaluable tool to downregulate gene expression in a variety of organisms, it is now evident that RNAi extends its tentacles into both the nucleus and the cytoplasm and is involved in a variety of gene silencing phenomena. Here we review the current status of RNAi in protozoan parasites that cause diseases of considerable medical and veterinary importance throughout Africa, Asia and the Americas. RNAi was first discovered in Trypanosoma brucei, a species of the family Trypanosomatidae, and it rapidly became the method of choice to downregulate gene expression in these organisms. At the same time, mechanistic studies exposed a role for RNAi in the control of retroposon transcript abundance. Whereas RNAi is also present in T. congolense, other members of the same family of organisms, namely T. cruzi and Leishmania major, are RNAi-negative. In apicomplexan parasites, there is experimental evidence for RNAi in Plasmodium, but this is not supported by their genetic make up. In contrast, the genome of Toxoplasma gondii harbours gene candidates with convincing similarity to 'classical' RNAi genes. Thus, as previously shown in fungi, protozoan parasites are genetically heterogeneous as far as the RNAi pathway is concerned. Finally, database mining predicts that Entamoeba histolytica and Giardia intestinalis have an RNAi pathway and the presence of RNAi genes in Giardia supports the view that gene silencing by dsRNA appeared very early during evolution of the eukaryotic lineage.
Blocking of HIV-1 Infectivity by a Soluble, Secreted Form of the CD4 Antigen (1987)

The initial event in the infection of human T lymphocytes, macrophages, and other cells by human immunodeficiency virus (HIV-1) is the attachment of the HIV-1 envelope glycoprotein gp120 to its cellular receptor, CD4. As a step toward designing antagonists of this binding event, soluble, secreted forms of CD4 were produced by transfection of mammalian cells with vectors encoding versions of CD4 lacking its transmembrane and cytoplasmic domains. The soluble CD4 so produced binds gp120 with an affinity and specificity comparable to intact CD4 and is capable of neutralizing the infectivity of HIV-1. These studies reveal that the high-affinity CD4-gp120 interaction does not require other cell or viral components and may establish a novel basis for therapeutic intervention in the acquired immune deficiency syndrome (AIDS).
A CD8 DE loop peptide analog prevents graft-versus-host disease in a multiple minor histocompatibility antigen-mismatched bone marrow transplantation model (2004)

Donor CD8(+) T cells can be potent mediators of graft-versus-host disease (GVHD) after allogeneic hematopoietic cell transplantation to either major histocompatibility complex (MHC) class I-or multiple minor histocompatibility antigen-mismatched recipients. To develop small molecular inhibitors of CD8(+) T-cell activity, theoretical structural analysis of the human CD8 alpha molecule was previously used to identify potential functional surface epitopes that interact with the MHC class I molecule. The DE loop (p71-78) was identified as such a target region, and a panel of synthetic cyclized peptide mimics of this region were tested for their inhibitory effects on cytotoxic T lymphocyte activity in human cell-mediated lympholysis assays. Peptide 1109 (CKRLGDTFVC) was most effective at inhibiting specific target cell lysis. Accordingly, studies were conducted to determine whether there was sufficient cross-species homology in the DE loop region and its nonpolymorphic interactive site on the beta(2)-microglobulin domain of the MHC class I molecule to allow similar inhibition of murine CD8(+) cytotoxic T lymphocyte activity. On the basis of strong in vitro inhibitory activity of 1109 in the murine system, the capacity of the peptide to inhibit in vivo CD8(+) T-cell effector functions in skin and hematopoietic stem cell transplantation models was examined. In the C57BL/6 anti-bm1 skin allograft rejection model, across an MHC class I barrier, a single injection of 1109 at the time of transplantation significantly prolonged graft survival. Moreover, 1109 administered at the time of transplantation in the multiple minor histocompatibility antigen-disparate B10.BR-->CBA GVHD model significantly prolonged the survival of lethally irradiated mice that underwent transplantation with donor bone marrow cells and CD8(+) T cells. Histopathologic analysis confirmed that mice treated with the synthetic peptide exhibited diminution of epithelial target cell injury. Specificity of the peptide effect was evidenced by draining lymph node cells from B10.BR mice that had been challenged with CBA lymphocytes and simultaneously treated with 1109. These cells could not generate secondary proliferative responses in vitro upon stimulation with CBA splenocytes but could respond to third-party C57BL/6 stimulation. Thus, the 1109 peptide has potential application in the prevention of CD8-mediated GVHD development.
Loss of heterozygosity in epithelial cells obtained by bronchial brushing: clinical utility in lung cancer. (1999)

To determine whether loss of heterozygosity (LOH) could be a useful diagnostic test for lung cancer, we evaluated LOH in cells obtained from bronchial brushings. Cells from radiographically normal and abnormal lungs were obtained from 55 patients undergoing diagnostic bronchoscopy. Among 38 patients with lung cancer, LOH was present in at least one chromosomal locus in 79%, whereas cytology was positive for malignant cells in 37%. LOH was not restricted to the airway containing the tumor; fifty-three percent of the cancer patients had LOH in the contralateral lung, as did 59% of patients without lung cancer. There was an association between the extent of LOH and proximity to the cancer. The LOH score, which combined measures of fractional allelic loss and percentage of cells with allelic loss, was greater in subjects with positive cytology and on the side of the tumor. A LOH score >10 was positive in 58% of tumor-bearing lungs, in 13% of the contralateral lungs in cancer patients, and in no patients without cancer. Our results suggest that extensive and widespread allelic loss, as indicated by a high LOH score, may be diagnostic of lung cancer. Additional studies will be needed to clarify the clinical potential of using bronchial epithelial cell LOH as a biomarker and diagnostic test for lung cancer.
Recycling side-effects into clinical markers for drug repositioning (2012)

Side-effects are the unintended consequence of therapeutic treatments, but they can also be seen as valuable read-outs of drug effects in humans; these effects are difficult to infer or predict from pre-clinical models. Indeed, some studies suggest that drugs with similar side-effect profiles may also share therapeutic properties through related mechanisms of action. A recent publication exploits this concept to systematically investigate new indications for already marketed drugs, and presents a strategy to get the most out of the tiny portion of chemicals that have proved to be effective and safe.
Trends in incidence and mortality in rheumatoid arthritis in Rochester, Minnesota, over a forty‐year period (2002)

The secular trends demonstrated in this study population, including the progressive decline in the incidence of RA over the last 40 years, suggest that an environmental factor may play a role in the etiology of RA.
Inhibition of kinesin synthesis and rapid anterograde axonal transport in vivo by an antisense oligonucleotide (1993)

Synthetic antisense oligonucleotides have been used to inhibit specific protein synthesis in vivo. Antisense oligonucleotides directed to kinesin heavy chain were injected into the vitreous of anesthetized rabbits in order to assess the effects on transport in the retinal ganglion cells whose axons form the optic nerve. The antisense oligonucleotide specifically inhibited retinal kinesin synthesis by 82 +/- 7% (n = 4). The rapid axonal transport of the membrane proteins into the optic nerve was concomitantly inhibited by 70 +/- 10% (n = 4). These results provide direct evidence for the specific role of kinesin in rapid anterograde transport in vivo and indicate the utility of antisense oligonucleotides to explore neuronal dynamics in a specific neuronal cell type in a living animal.
Nucleotide sequence of the 26S mRNA of Sindbis virus and deduced sequence of the encoded virus structural proteins. (1981)

The nucleotide sequence of intracellular 26S mRNA of Sindbis virus has been determined by direct sequence analysis of the cDNA made to this RNA with reverse transcriptase. From this, the amino acid sequences of the encoded virus structural proteins, which include a basic capsid protein and two integral membrane glycoproteins, have been deduced. The features of these proteins as related to their functions are discussed. We suggest that three proteases are required to produce these proteins from their polyprotein precursor: a viral protease, which functions in the cytosol to release the capsid protein, signalase, which makes two cleavages to separate the glycoproteins; and a protease of the Golgi complex that cleaves after double basic residues, to process the precursor form of one of the glycoproteins.
Barth syndrome, a human disorder of cardiolipin metabolism (2006)

Barth syndrome is an X-linked recessive disease caused by mutations in the tafazzin gene. Patients have reduced concentration and altered composition of cardiolipin, the specific mitochondrial phospholipid, and they have variable clinical findings, often including heart failure, myopathy, neutropenia, and growth retardation. This article provides an overview of the molecular basis of Barth syndrome. It is argued that tafazzin, a phospholipid acyltransferase, is involved in acyl-specific remodeling of cardiolipin, which promotes structural uniformity and molecular symmetry among the cardiolipin molecular species. Inhibition of this pathway leads to changes in mitochondrial architecture and function.
Foxn4 directly regulates tbx2b expression and atrioventricular canal formation (2008)

Cardiac chamber formation represents an essential evolutionary milestone that allows for the heart to receive (atrium) and pump (ventricle) blood throughout a closed circulatory system. Here, we reveal a novel transcriptional pathway between foxn4 and tbx genes that facilitates this evolutionary event. We show that the zebrafish gene slipjig, which encodes Foxn4, regulates the formation of the atrioventricular (AV) canal to divide the heart. sli/foxn4 is expressed in the AV canal, and its encoded product binds to a highly conserved tbx2 enhancer domain that contains Foxn4- and T-box-binding sites, both necessary to regulate tbx2b expression in the AV canal.
Scaling Memory-Augmented Neural Networks with Sparse Reads and Writes (2016)

Neural networks augmented with external memory have the ability to learn algorithmic solutions to complex tasks. These models appear promising for applications such as language modeling and machine translation. However, they scale poorly in both space and time as the amount of memory grows --- limiting their applicability to real-world domains. Here, we present an end-to-end differentiable memory access scheme, which we call Sparse Access Memory (SAM), that retains the representational power of the original approaches whilst training efficiently with very large memories. We show that SAM achieves asymptotic lower bounds in space and time complexity, and find that an implementation runs $1,\!000\times$ faster and with $3,\!000\times$ less physical memory than non-sparse models. SAM learns with comparable data efficiency to existing models on a range of synthetic tasks and one-shot Omniglot character recognition, and can scale to tasks requiring $100,\!000$s of time steps and memories. As well, we show how our approach can be adapted for models that maintain temporal associations between memories, as with the recently introduced Differentiable Neural Computer.
Epidemiology of shigellosis in Lagos, Nigeria: trends in antimicrobial resistance. (2001)

Antimicrobial susceptibility of Shigella spp. and Escherichia coli, isolated from diarrhoeal patients in Lagos, was studied from March 1999 to February 2000. Four hundred fifty-nine isolates were identified as shigellae (62) and E. coli (397). Shigella flexneri, S. dysenteriae, S. boydii, and S. sonnei accounted, respectively, for 51.6%, 17.7%, 17.7%, and 13% of the total number of shigellae isolated. Eleven cases of shigellosis occurred in the age group of 0-9 years, 22 cases in the age group of 10-19 years, and 29 cases in the age group of > or = 20 years. Of the 397 E. coli isolates, 11 were enteropathogenic E. coli (EPEC), and 7 of these strains were isolated with shigellae from stools of patients aged 0-9 year(s) (71.4%) and 10-19 years (28.6%). Over 70% of the Shigella isolates were resistant to two or more drugs, including ampicillin and tetracycline. Twenty-one distinct multidrug resistance patterns were observed in these isolates. During 1990-2000, resistance to ampicillin increased from 70% to 90%, co-trimoxazole from 77% to 85%, chloramphenicol from 71% to 77%, streptomycin from 71% to 79%, and nalidixic acid from 0% to 11.3%. Resistance to tetracycline decreased from 89% to 79% but with MIC50 and MIC90 values outside the susceptible range. While resistance to ciprofloxacin and ofloxacin remained nil with MIC50 and MIC90 values of 0.008 and 0.0016 microgram/mL respectively. The results of this study revealed the endemicity of shigellosis with S. flexneri as the predominant serogroup in Lagos. Children and young adults were at a higher risk of severe shigellosis. The results also suggest that ampicillin, tetracycline, co-trimoxazole, and streptomycin should not be used as the first-line drugs in the treatment of shigellosis. Nalidixic acid should still be selectively used for treatment, while ciprofloxacin and ofloxacin can be ideal alternatives.
Ventilator-induced Lung Injury Is Mediated by the NLRP3 Inflammasome (2012)

Mechanical ventilation induced a NLRP3 inflammasome dependent pulmonary inflammatory response. NLRP3 inflammasome deficiency partially protected mice from VILI.
VLSI architecture design of a versatile variable length decoding chip for real-time video codecs (2002)

The authors describe a VLSI architecture of a versatile variable length decoder suitable for several-coding algorithms. This design can achieve real-time performance for video codecs and is based on the CCITT recommendation H.261 format. It includes an extra module to decode the variable length codes (VLC) defined by the International Organization for Standardization (ISO) Joint Photographic Experts Group (JPEG). Moreover, taking into account the fact that some VLCs used by H.261 and/or JPEG might be incorporated into the evolving ISO Moving Picture Experts Group (MPEG) algorithm, the design uses (a) PLAs for fixed VLC tables which can be shared by different algorithms and (b) content addressable memory (CAM) for downloadable tables to accommodate variations. The authors also describe a deformatter, implemented by a finite-state machine, whose function is to extract header information embedded in the coded bit-stream.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>