gebhart/patrepeval huggingface dataset:
Clostridium difficile Infection (1998)

Clostridium difficile infection is associated with broad-spectrum antibiotic therapy and is the most common cause of infectious diarrhea in hospital patients. Pathogenic strains of C. difficile produce two protein exotoxins, toxin A and toxin B, which cause colonic mucosal injury and inflammation. Infection may be asymptomatic, cause mild diarrhea, or result in severe pseudomembranous colitis. Diagnosis depends on the demonstration of C. difficile toxins in the stool. The first step in management is to discontinue the antibiotic that caused diarrhea. If diarrhea and colitis are severe or persistent, oral metronidazole is the treatment of choice. Oral vancomycin is also effective, but it is more expensive than metronidazole and its widespread use may encourage the proliferation of vancomycin-resistant nosocomial bacteria. Diarrhea and colitis usually improve within three days after a patient starts taking metronidazole or vancomycin, but 20% suffer a relapse of diarrhea when these agents are discontinued.
Effects of Setting on Window Preferences and Factors Associated with Those Preferences (1989)

Window preference research on a few settings has found that windows are generally preferred and that larger windows are preferred over smaller ones. No theoretical model of window preferences, however, has been proposed. The present experiment was designed to investigate window preferences across a large variety of common spaces and to examine reasons orfactors that may underlie these preferences with the ultimate goal of predicting them. Window preferences, in terms of size, number, and degree of transparency were made for 14 common spaces. Subjects then indicated the factors underlying their specific preferences from a list of 18 potential factors. Results showed that both window preferences and factors vary more widely than previous research would indicate. More important, however, it was demonstrated that the amount of windows desired in a space can be reliably predicted by knowing how important specific factors (e.g., having a view or good ventilation) are to individuals in that space.
A study of branch prediction strategies (1998)

In high-performance computer systems. performance losses due to conditional branch instructrons can be minrmized by predicting a branch outcome and fetching, decoding, and/or issuing subsequent instructions before the actual outcome is known. This paper discusses branch prediction strategies wrth the goal of maxtmizing prediction accuracy. First. currently used techniques are discussed and analyzed using instruction tmce data. Then, new techniques are proposed and are shown to provide greater accuracy and more flexibility at low cost.
Elevated cord serum IgE increases the risk of aeroallergen sensitization without increasing respiratory allergic symptoms in early childhood (1999)

Cord IgE is better than family history for predicting atopy as defined by allergen sensitization and this predictive value can be further increased by combining cord IgE with paternal atopy.
STAT3 Activation in Skeletal Muscle Links Muscle Wasting and the Acute Phase Response in Cancer Cachexia (2011)

These results suggest that the STAT3 transcriptome is a major mechanism for wasting in cancer. Through IL-6/STAT3 activation, skeletal muscle is induced to synthesize acute phase proteins, thus establishing a molecular link between the observations of high IL-6, increased acute phase response proteins and muscle wasting in cancer. These results suggest a mechanism by which STAT3 might causally influence muscle wasting by altering the profile of genes expressed and translated in muscle such that amino acids liberated by increased proteolysis in cachexia are synthesized into acute phase proteins and exported into the blood.
Glucosylglycerol accumulation during salt acclimation of two unicellular cyanobacteria (1992)

SUMMARY: A turbidostat culture technique was used to study the effects of different salt shocks on the freshwater cyanobacteria Synechocystis sp. strain PCC 6803 and Microcystis firma. Shocks were performed either suddenly or gradually, on both unacclimated cultures and those pre-acclimated to 0·77 M-NaCl. All suddenly shocked cultures exhibited a decline in growth after a few hours, characterized by severely decreased metabolic activities (e.g. photosynthesis, respiration, glucose-6-phosphate dehydrogenase activity) and a time course of restoration which coincided with the accumulation of glucosylglycerol. Additionally, all untreated cultures had a late (after a few days) growth depression, distinguished by the stagnation of cell division. This was overcome by physiological adaptation of the whole cells or selection of cells with superior salt tolerance. The different types of growth depressions and the unique pattern of glucosylglycerol accumulation led to the conclusion that glucosylglycerol was necessary to maintain metabolic processes, but that this alone cannot account for successful salt acclimation.
Standardisation of the Rey Complex Figure Test in New Zealand Children and Adolescents (2003)

X-ray microdiffraction utilizing Fresnel zone plate focusing optics has been used to study microstructural properties of individual 90 degree ferroelectric domains in BaTiO3. Diffraction measurements at a microfocused spot resolution of 0.3 microm over domain widths of approximately 10 microm unambiguously reveal features of lattice buckling, rotation, and strain near domain boundaries. Our results may be understood within the context of bound residual strain due to lattice mismatch and elastic interactions between neighboring domains.
Monoclonal antibodies in clinical immunology. (1981)

Advances in clinical immunodiagnostics resulting from the application of hybridoma technology are starting to appear. Monoclonal antibodies are beginning to displace their antiquated progenitors, polyclonal antisera, in many facets of immunology. Their homogeneity, specificity, and availability make hybridoma-derived antibodies the immunological reagents of the future in immunoassays, immuno-affinity chromatography, immunotherapy, and areas yet to be defined.
In vivo delivery of caspase-8 or Fas siRNA improves the survival of septic mice (2005)

Although studies have shown increased evidence of death receptor-driven apoptosis in intestinal lymphoid cells, splenocytes, and the liver following the onset of polymicrobial sepsis, little is known about the mediators controlling this process or their pathologic contribution. We therefore attempted to test the hypothesis that the hydrodynamic administration of small interfering RNA (siRNA) against the death receptor, Fas or caspase-8, should attenuate the onset of morbidity and mortality seen in sepsis, as produced by cecal ligation and puncture (CLP). We initially show that in vivo administration of green fluorescent protein (GFP) siRNA in GFP transgenic mice results in a decrease in GFP fluorescence in most tissues. Subsequently, we also found that treating septic nontransgenic mice with siRNA targeting Fas or caspase-8 but not GFP (used as a control here) decreased the mRNA, in a sustained fashion up to 10 days, and protein expression of Fas and caspase-8, respectively. In addition, transferase-mediated dUTP (deoxyuridine triphosphate) nick end labeling (TUNEL) and active caspase-3 analyses revealed a decrease in apoptosis in the liver and spleen but not the thymus following siRNA treatment. Indices of liver damage were also decreased. Finally, the injection of Fas or caspase-8 given not only 30 minutes but up to 12 hours after CLP significantly improved the survival of septic mice.
Neuroprotection by bromocriptine against 1‐methyl‐4‐phenyl‐1,2,3,6‐tetrahydropyridine‐induced neurotoxicity in mice 1 (1998)

Mice were treated with 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP; 30 mg/kg i.p. twice, 16 h apart). This resulted in changes in motor performance and toxic insult of nigral neurons as evidenced by dopamine depletion in nucleus caudatus putamen. In vitro and in vivo treatment of MPTP caused the generation of hydroxyl radicals (.OH) as measured by a sensitive salicylate hydroxylation procedure. A dopamine agonist, bromocriptine (10 microM and 10 mg/kg i.p.), blocked .OH formation caused by MPTP in vitro (20 microM) and in vivo (30 mg/kg i.p.). An MPTP-induced increase in the activity of catalase and superoxide dismutase in substantia nigra on the seventh day was reduced by bromocriptine pretreatment. Bromocriptine blocked MPTP-induced behavioral dysfunction as well as glutathione and dopamine depletion, indicating its potent neuroprotective action. This study suggests that bromocriptine stimulates antioxidant mechanisms in the brain and acts as a free radical scavenger in addition to its action at dopamine receptors, thus indicating its strength as a valuable neuroprotectant.
Parameter estimation for the calibration and variance stabilization of microarray data (2003)

We derive and validate an estimator for the parameters of a transformation for the joint calibration (normalization) and variance stabilization of microarray intensity data. With this, the variances of the transformed intensities become approximately independent of their expected values. The transformation is similar to the logarithm in the high intensity range, but has a smaller slope for intensities close to zero. Applications have shown better sensitivity and specificity for the detection of differentially expressed genes. In this paper, we describe the theoretical aspects of the method. We incorporate calibration and variance-mean dependence into a statistical model and use a robust variant of the maximum-likelihood method to estimate the transformation parameters. Using simulations, we investigate the size of the estimation error and its dependence on sample size and the presence of outliers. We find that the error decreases with the square root of the number of probes per array and that the estimation is robust against the presence of differentially expressed genes. Software is publicly available as an R package through the Bioconductor project (http://www.bioconductor.org).
Role of serotonin in the pathophysiology of depression: focus on the serotonin transporter (1994)

Considerable evidence has accrued in the last two decades to support the hypothesis that alterations in serotonergic neuronal function in the central nervous system occur in patients with major depression. These findings include the following: (a) reduced cerebrospinal fluid (CSF) concentrations of 5-hydroxyindoleacetic acid (5-HIAA), the major metabolite of serotonin (5-HT) in drug-free depressed patients; (b) reduced concentrations of 5-HT and 5-HIAA in postmortem brain tissue of depressed and (or) suicidal patients; (c) decreased plasma tryptophan concentrations in depressed patients and a profound relapse in remitted depressed patients who have responded to a serotonergic antidepressant when brain tryptophan availability is reduced; (d) in general, all clinically efficacious antidepressants augment 5-HT neurotransmission following chronic treatment; (e) clinically efficacious antidepressant action by all inhibitors of 5-HT uptake; (f) increases in the density of 5-HT2 binding sites in postmortem brain tissue of depressed patients and suicide victims, as well as in platelets of drug-free depressed patients; (g) decreased number of 5-HT transporter (determined with [3H]imipramine or [3H]paroxetine) binding sites in postmortem brain tissue of suicide victims and depressed patients and in platelets of drug-free depressed patients. In our studies, this reduction in platelet 5-HT transporter binding is not due to prior antidepressant treatment of hypercortisolemia and is not observed in mania, Alzheimer disease, schizophrenia, panic disorder, fibromyalgia, or atypical depression. In a pilot study, this deficit predicted treatment response to an experimental antidepressant. These findings support the hypothesis that alterations in 5-HT neurons play a role in the pathophysiology of depression.
Biphasic Dose Response in Low Level Light Therapy (2009)

The use of low levels of visible or near infrared light for reducing pain, inflammation and edema, promoting healing of wounds, deeper tissues and nerves, and preventing cell death and tissue damage has been known for over forty years since the invention of lasers. Despite many reports of positive findings from experiments conducted in vitro, in animal models and in randomized controlled clinical trials, LLLT remains controversial in mainstream medicine. The biochemical mechanisms underlying the positive effects are incompletely understood, and the complexity of rationally choosing amongst a large number of illumination parameters such as wavelength, fluence, power density, pulse structure and treatment timing has led to the publication of a number of negative studies as well as many positive ones. A biphasic dose response has been frequently observed where low levels of light have a much better effect on stimulating and repairing tissues than higher levels of light. The so-called Arndt-Schulz curve is frequently used to describe this biphasic dose response. This review will cover the molecular and cellular mechanisms in LLLT, and describe some of our recent results in vitro and in vivo that provide scientific explanations for this biphasic dose response.
Quantitative Determination of Lentiviral Vector Particle Numbers by Real-Time PCR (2001)

Here, we describe a quantitative, DNA-based, real-time PCR approach to determine the number of lentivirus particles that are present in vector preparations. In this approach, the minus strong-stop cDNA fragment that is present in viral capsids serves as template for PCR. Using this technology, we found that only 0.1%-1% of the virus particles that are present in vector preparations are infectious. The approach described here is rapid, reliable, and simple in concept and can be used to estimate both vector particles in supernatants and the number of infectious particles. Also, this approach can easily be adapted to a high-throughput system by using 96-well plates and a 2-h running time.
Nucleocytoplasmic Shuttling of Bovine Herpesvirus 1 UL47 Protein in Infected Cells (2005)

Previous studies with transfected cells have shown that the herpes simplex virus type 1 (HSV-1) and bovine herpesvirus 1 (BHV-1) UL47 proteins shuttle between the nucleus and the cytoplasm. HSV-1 UL47 has also been shown to bind RNA. Here we examine the BHV-1 UL47 protein in infected cells using a green fluorescent protein-UL47-expressing virus. We show that UL47 is detected in the nucleus early in infection. We use fluorescence loss in photobleaching to show that nuclear UL47 undergoes rapid nucleocytoplasmic shuttling. Furthermore, we demonstrate that actinomycin D inhibits the reaccumulation of UL47 in the nuclei of infected cells. These results suggest that UL47 exhibits behavior similar to that of previously characterized RNA-transporting proteins.
Point Mutations in Human GLI3 Cause Greig Syndrome (1997)

Greig cephalopolysyndactyly syndrome (GCPS, MIM 175700) is a rare autosomal dominant developmental disorder characterized by craniofacial abnormalities and post-axial and pre-axial polydactyly as well as syndactyly of hands and feet. Human GLI3, located on chromosome 7p13, is a candidate gene for the syndrome because it is interrupted by translocation breakpoints associated with GCPS. Since hemizygosity of 7p13 resulting in complete loss of one copy of GLI3 causes GCPS as well, haploinsufficiency of this gene was implicated as a mechanism to cause this developmental malformation. To determine if point mutations within GLI3 could be responsible for GCPS we describe the genomic sequences at the boundaries of the 15 exons and primer pair sequences for mutation analysis with polymerase chain reaction-based assays of the entire GLI3 coding sequences. In two GCPS cases, both of which did not exhibit obvious cytogenetic rearrangements, point mutations were identified in different domains of the protein, showing for the first time that Greig syndrome can be caused by GLI3 point mutations. In one case a nonsense mutation in exon X generates a stop codon truncating the protein in the C-H link of the first zinc finger. In the second case a missense mutation in exon XIV causes a Pro-->Ser replacement at a position that is conserved among GLI genes from several species altering a potential phosphorylation site.
Isolation and identification of short nucleotide sequences that affect translation initiation in Saccharomyces cerevisiae (2003)

In previous studies, we demonstrated the sufficiency of short nucleotide sequences to facilitate internal initiation of translation in mammalian cells. By using a selection methodology, we have now identified comparable sequences in Saccharomyces cerevisiae. For these studies, a library of constructs expressing dicistronic mRNAs with the HIS3 gene as the second cistron and 18 random nucleotides in the intercistronic region was introduced into a yeast strain in which the endogenous HIS3 gene was deleted. Untransformed cells or those containing the parent construct failed to grow on medium lacking histidine. Intercistronic sequences recovered from cells that did grow were evaluated by using various criteria. Fifty-six of the 18-nt sequences (approximately 1/400,000) functioned as synthetic internal ribosome entry sites (IRESes). The 14 most active sequences allowed growth in the presence of 0.1-0.6 mM 3-amino-1,2,4-triazole, a competitive inhibitor of the HIS3 gene product. In addition, eight sequences were identified that were not IRESes, but that enhanced HIS3 expression by an alternative mechanism that depended on the 5' end of the mRNA and appeared to involve either shunting or reinitiation. Comparisons among the 56 selected IRESes identified eight significant sequence matches containing up to 10 nucleotides. Many of the selected sequences also contained extensive complementary matches to yeast 18S rRNA, some at overlapping sites. The identification of cis sequences that facilitate translation initiation in yeast enables detailed biochemical and genetic analyses of underlying mechanisms and may have practical applications for bioengineering.
Method for detection of specific RNAs in agarose gels by transfer to diazobenzyloxymethyl-paper and hybridization with DNA probes. (1977)

We describe a technique for transferring electrophoretically separated bands of RNA from an agarose gel to paper strips. The RNA is coupled covalently to diazobenzyloxymethyl groups on the paper. After transfer and appropriate treatment of the paper to destroy remaining diazo groups, specific RNA bands can be detected by hybridization with 32P-labeled DNA probes followed by autoradiography. This procedure allows detection of specific RNA bands with high sensitivity and low background.
Development of Parthenogenetic Rat Embryos1 (2003)

In an effort to establish cloning technology for the rat, we tested several methods (electric stimulation, treatment with ethanol or strontium) for the parthenogenetic activation of rat oocytes. We observed marked individual differences among rats of the outbred Wistar strain in their ability to yield activatable oocytes. These differences were independent of the activation protocol and may be due to a genetic predisposition that is crucial for the parthenogenetic activation of oocytes. The activation of oocytes was dependent upon the time between superovulation of the donor animal and the collection of the embryos. Aged oocytes (derived about 24 h after superovulation) were more prone to activation by each method than were younger oocytes, and some even underwent spontaneous activation without treatment and exhibited pronuclear formation and blastocyst development. All activation methods were effective in generating parthenogenetic rat embryos, and rat parthenotes developed until implantation. However, in general, short-term (15 min) and long-term (2 h) strontium treatment was superior to stimulation by ethanol or electric pulse for parthenogenetic activation. These results will be helpful in achieving successful cloning in the rat.
从安然破产事件析“信息化”泡沫 (2002)

早在B2B这个名词出现以前,安然公司就已经在做企业间的电子商务了。1999年,安然公司搞了个在线电子商务平台,成为世界上最大的BZB电子商务平台。安然从薄利的天然气经营商摇身一变成为高利能源交易商,极大地提高了公司在能源管理方面的能力,被奉为信息化的楷模、最成功的电子商务应用范例……然而,今天安然倒下了。安然在管理信息化及电子商务应用方面的
Notecards in a nutshell (1986)

NoteCards is an extensible environment designed to help people formulate, structure, compare, and manage ideas. NoteCards provides the user with a “semantic network” of electronic notecards interconnected by typed links. The system provides tools to organize, manage, and display the structure of the network, as well as a set of methods and protocols for creating programs to manipulate the information in the network. NoteCards is currently being used by more than 50 people engaged in idea processing tasks ranging from writing research papers through designing parts for photocopiers.
Melioidosis: the tip of the iceberg? (1991)

For nearly 80 years clinical melioidosis has been considered a rare disease. This bacterial infection is caused by Pseudomonas pseudomallei, a saprophyte found in soil and surface water of endemic areas. Consequently, those who have most contact with soil, the rural poor, are likely to be at greatest risk of infection. Since the diversity of clinical manifestations necessitates the isolation and identification of the causative organism for a definitive diagnosis of melioidosis and the population at greatest risk within endemic areas rarely have access to an appropriate level of health care, the disease has probably been underrecognized. Melioidosis is now known to be an important cause of human morbidity and mortality in Thailand, and this may be true throughout Southeast Asia, which is usually regarded as the main endemic area for the disease. In Australia, melioidosis causes a smaller number of human infections, while disease among livestock has important economic and possible public health implications. Sporadic reports of the infection indicate its presence in several other tropical regions: in the Indian subcontinent, Africa, and Central and South America. Clinical melioidosis may be highly prevalent in these areas, but underdiagnosed as a result of a lack of awareness of the clinical and microbiological features of the disease, or simply because of a lack of health care facilities. Furthermore, during the last two decades the importation and transmission of melioidosis within nontropical zones have been documented. The causative organism is not difficult to grow, and modern antibiotics have improved disease prognosis. Further studies are needed to determine the true worldwide distribution and prevalence of melioidosis so that improved therapeutic and preventive measures can be developed and applied.
Reducing repair traffic for erasure coding-based storage via interference alignment (2009)

We consider the problem of recovering from a single node failure in a storage system based on an (n, k) MDS code. In such a scenario, a straightforward solution is to perform a complete decoding, even though the data to be recovered only amount to 1/kth of the entire data. This paper presents techniques that can reduce the network traffic incurred. The techniques perform algebraic alignment so that the effective dimension of unwanted information is reduced.