gebhart/patrepeval huggingface dataset:
Enzymatic Degradation of Insoluble Carbohydrates (1996)

Amylases, cellulases, chitinases, lysozymes and xylanases are all insoluble polysaccharide hydrolases. Many of these enzymes possess a separate substrate binding domain that is pointed to the catalytic domain by a hinge peptide. All of them contain multiple binding sites for sugar monomers (from four to eight) in their active sites and either two or three carboxyl side chains that function in catalysis. There are three amylase families, nine cellulase families, two chitinase families, five lysozyme families and two xylanase families. The enzymes in some families invert the conformation of the glycoside oxygen during hydrolysis while the enzymes in the other families retain the conformation. The structure of an inverting endocellulase, Thermomonospora fusca E2, has been determined by X-ray crystallography at 1.18 Å resolution. It has an open active site cleft, while CBHII which is an exocellulase with the same polypeptide chain fold has its active site in a tunnel. Several E2 mutants have been isolated and characterized to help determine its catalytic mechanism.
Utilizing quantized feedback information in orthogonal space-time block coding (2002)

Previously, space-time codes have been developed that achieve a large portion of the capacity available in communication systems equipped with multiple transmit and receive antennas. These codes are designed under the assumption that the transmitter has no knowledge about the channel. In this work, on the other hand, we consider how the presence of vector quantized channel information obtained from a feedback link may be utilized for improving the performance of a space-time code. The transmission scheme we propose takes the non-perfect nature of the channel information into account while combining the benefits of conventional beamforming with those given by orthogonal space-time block codes. Simulation results demonstrate significant gains over conventional methods and also robustness to feedback channel errors.
Mapping and comparison of the interaction sites on the Fc region of IgG responsible for triggering antibody dependent cellular cytotoxicity (ADCC) through different types of human Fcγ receptor (1992)

In the present study 3-iodo-4-hydroxy-5-nitrophenacetyl (NIP)-specific antibodies were compared for induction of antibody dependent lysis of NIP-derivatised red blood cells effected by pre-stimulated U937 or HL-60 cells and by K cells. The chimaeric antibodies have heavy chains corresponding to human IgG subclasses 1-4, and include site-directed mutants of IgG3 as well as the aglycosylated form of IgG3; a mouse IgG2b antibody and a site-directed mutant IgG2b were also examined. rIFN stimulated U937 or HL-60 cells express increased levels of Fc gamma R1 compared to unstimulated cells; PMA stimulated HL-60 and U937 cells express an increased level of Fc gamma R11 compared to unstimulated cells; K cells express Fc gamma R111. Using these effector cell populations and the target cells mentioned above, we have compared anti-NIP antibodies with different heavy chain constant domains for their ability to induce ADCC through human Fc gamma R1, Fc gamma R11 and Fc gamma R111. The results suggest that all three human Fc gamma receptors appear to recognise a binding site on IgG within the lower hinge (residues 234-237) and trigger ADCC via this site, but that each receptor sees this common site in a different way. The possibility that other amino acid residues also participate in the binding/triggering site(s) cannot be excluded.
Clock distribution networks in synchronous digital integrated circuits (2001)

Clock distribution networks synchronize the flow of data signals among synchronous data paths. The design of these networks can dramatically affect system-wide performance and reliability. A theoretical background of clock skew is provided in order to better understand how clock distribution networks interact with data paths. Minimum and maximum timing constraints are developed from the relative timing between the localized clock skew and the data paths. These constraint relationships are reviewed, and compensating design techniques are discussed. The field of clock distribution network design and analysis can be grouped into a number of subtopics: 1) circuit and layout techniques for structured custom digital integrated circuits; 2) the automated layout and synthesis of clock distribution networks with application to automated placement and routing of gate arrays, standard cells and larger block-oriented circuits; 3) the analysis and modeling of the timing characteristics of clock distribution networks; and 4) the scheduling of the optimal timing characteristics of clock distribution networks based on architectural and functional performance requirements. Each of these areas is described the clock distribution networks of specific industrial circuits are surveyed and future trends are discussed.
Gender differences in sleep disorders (2006)

Gender differences in sleep become apparent after the onset of puberty. Menstrual cycles, pregnancy, and menopause can alter sleep architecture. Gender-related differences in sleep disorders, such as obstructive sleep apnea, insomnia, and restless legs syndrome, include differences in prevalence, pathophysiology, clinical presentation, and response to therapy.
Polymer Nanocomposites Containing Carbon Nanotubes (2006)

We review the present state of polymer nanocomposites research in which the fillers are single-wall or multiwall carbon nanotubes. By way of background we provide a brief synopsis about carbon nanotube materials and their suspensions. We summarize and critique various nanotube/polymer composite fabrication methods including solution mixing, melt mixing, and in situ polymerization with a particular emphasis on evaluating the dispersion state of the nanotubes. We discuss mechanical, electrical, rheological, thermal, and flammability properties separately and how these physical properties depend on the size, aspect ratio, loading, dispersion state, and alignment of nanotubes within polymer nanocomposites. Finally, we summarize the current challenges to and opportunities for efficiently translating the extraordinary properties of carbon nanotubes to polymer matrices in hopes of facilitating progress in this emerging area.
Negative regulatory approaches to the attenuation of Toll-like receptor signaling (2013)

Toll-like receptors (TLRs) are pivotal components of the innate immune response, which is responsible for eradicating invading microorganisms through the induction of inflammatory molecules. These receptors are also involved in responding to harmful endogenous molecules and have crucial roles in the activation of the innate immune system and shaping the adaptive immune response. However, TLR signaling pathways must be tightly regulated because undue TLR stimulation may disrupt the fine balance between pro- and anti-inflammatory responses. Such disruptions may harm the host through the development of autoimmune and inflammatory diseases, such as rheumatoid arthritis and systemic lupus erythematosus. Several studies have investigated the regulatory pathways of TLRs that are essential for modulating proinflammatory responses. These studies reported several pathways and molecules that act individually or in combination to regulate immune responses. In this review, we have summarized recent advancements in the elucidation of the negative regulation of TLR signaling. Moreover, this review covers the modulation of TLR signaling at multiple levels, including adaptor complex destabilization, phosphorylation and ubiquitin-mediated degradation of signal proteins, manipulation of other receptors, and transcriptional regulation. Lastly, synthetic inhibitors have also been briefly discussed to highlight negative regulatory approaches in the treatment of inflammatory diseases.
WOUND HEALING AND COLLAGEN FORMATION (1965)

The uptake, intracellular transport, and secretion of protein by guinea pig wound fibroblasts was studied by electron microscope radioautography using L-proline-3,4-H3 as a tracer. Experiments were performed to determine the curve of concentration of free amino acid in the blood after intraperitoneal administration of the labeled proline. Radioautographs were quantitatively analyzed and the concentration of isotope, in grains per unit area, was determined for the following cellular and extracellular compartments: ergastoplasm, Golgi complex, peripheral cytoplasmic structures, and collagen. The concentration of label, expressed as number of grains per unit area of each subcellular system, reveals the period during which each cellular compartment is maximally labeled, and presents a clearer picture of the passage of the label through each of these compartments. The data demonstrate appearance of the label at maximum concentration in the ergastoplasm 15 minutes after injection, and this compartment remains maximally labeled for 2 hours. In the Golgi complex, concentration is not maximal until 60 minutes after injection of isotope, and appears to decrease before or at about the same rate as that of the ergastoplasm. The present experiment is consistent with previous light microscope radioautographic studies, and no storage phase was found in the fibroblasts. The findings are not simply consistent with a direct precursor-product relationship between the contents of the ergastoplasm and those of the Golgi complex. Morphologic observations of regions in the fibroblast interpretable as possible sites of communication between the ergastoplasm and the extracellular space, together with the kinetic studies, permit the suggestion of an alternate pathway of passage of at least some of the synthesized protein directly from the ergastoplasmic cisternae to the cell exterior.
Affine SKIP and DIRECT modes for efficient video coding (2012)

Higher-order motion models were introduced in video coding a couple of decades ago, but have not been widely used due to both difficulty in parameters estimation and their requirement of more side information. Recently, researchers have put them back into consideration. In this paper, the affine motion model is employed in SKIP and DIRECT modes to produce a better prediction. In affine SKIP/DIRECT, candidate predictors of the motion parameters are derived from the motions of neighboring coded blocks, with the best predictor determined by rate-distortion tradeoff. Extensive experiments have shown the efficiency of these new affine modes. No additional motion estimation is needed, so the proposed method is also quite practical.
Reconstitution of Mammary Gland Development In Vitro: Requirement of c-met and c-erbB2 Signaling for Branching and Alveolar Morphogenesis (1998)

We have established a cell culture system that reproduces morphogenic processes in the developing mammary gland. EpH4 mouse mammary epithelial cells cultured in matrigel form branched tubules in the presence of hepatocyte growth factor/scatter factor (HGF/SF), the ligand of the c-met tyrosine kinase receptor. In contrast, alveolar structures are formed in the presence of neuregulin, a ligand of c-erbB tyrosine kinase receptors. These distinct morphogenic responses can also be observed with selected human mammary carcinoma tissue in explant culture. HGF/SF-induced branching was abrogated by the PI3 kinase inhibitors wortmannin and LY294002. In contrast, neuregulin- induced alveolar morphogenesis was inhibited by the MAPK kinase inhibitor PD98059. The c-met-mediated response could also be evoked by transfection of a c-met specific substrate, Gab1, which can activate the PI3 kinase pathway. An activated hybrid receptor that contained the intracellular domain of c-erbB2 receptor suffices to induce alveolar morphogenesis, and was observed in the presence of tyrosine residues Y1028, Y1144, Y1201, and Y1226/27 in the substrate-binding domain of c-erbB2. Our data demonstrate that c-met and c-erbB2 signaling elicit distinct morphogenic programs in mammary epithelial cells: formation of branched tubules relies on a pathway involving PI3 kinase, whereas alveolar morphogenesis requires MAPK kinase.
Diagnosis and classification of diabetes mellitus: new criteria. (1998)

New recommendations for the classification and diagnosis of diabetes mellitus include the preferred use of the terms "type 1" and "type 2" instead of "IDDM" and "NIDDM" to designate the two major types of diabetes mellitus; simplification of the diagnostic criteria for diabetes mellitus to two abnormal fasting plasma determinations; and a lower cutoff for fasting plasma glucose (126 mg per dL [7 mmol per L] or higher) to confirm the diagnosis of diabetes mellitus. These changes provide an easier and more reliable means of diagnosing persons at risk of complications from hyperglycemia. Currently, only one half of the people who have diabetes mellitus have been diagnosed. Screening for diabetes mellitus should begin at 45 years of age and should be repeated every three years in persons without risk factors, and should begin earlier and be repeated more often in those with risk factors. Risk factors include obesity, first-degree relatives with diabetes mellitus, hypertension, hypertriglyceridemia or previous evidence of impaired glucose homeostasis. Earlier detection of diabetes mellitus may lead to tighter control of blood glucose levels and a reduction in the severity of complications associated with this disease.
A transgenic mouse line that develops early-onset invasive gastric carcinoma provides a model for carcinoembryonic antigen-targeted tumor therapy (2000)

In an attempt to obtain suitable in vivo models for optimizing new tumor therapy strategies for intestinal adenocarcinomas, carcinoembryonic antigen (CEA) promoter/SV40 T antigen gene constructs have been used to generate transgenic mice. One transgenic line (L5496), which contains a 424-bp CEA promoter/SV40 T antigen transgene, exclusively developed multi-focal carcinomas in the pyloric region of the stomach in 100% of the offspring. Tumors were already observable in 37-day-old animals as dysplastic cell foci within the mucosal layer. In 50-day-old mice, the tumor mass was mainly restricted to the mucosa with invasive growth into the submucosal tissue. The animals became moribund at 100-130 days of age due to blockage of the pylorus. At this time, the tumor had penetrated into the duodenum and had invaded all tissue layers within the stomach. In contrast to most other stomach tumor models, this one perfectly matches the development of the most common stomach cancers found in humans. Furthermore, after crossing these mice with mice that are transgenic for the human CEA gene, the double transgenic offspring revealed expression of CEA in the resulting tumors. Thus, as well as being a model for studying gastric carcinoma development and prevention, this system should provide a useful preclinical model for CEA-targeted gastric tumor therapy.
Exponential Isothermal Amplification of Nucleic Acids and Assays for Proteins, Cells, Small Molecules, and Enzyme Activities: An EXPAR Example (2018)

Isothermal exponential amplification techniques, such as strand-displacement amplification (SDA), rolling circle amplification (RCA), loop-mediated isothermal amplification (LAMP), nucleic acid sequence based amplification (NASBA), helicase-dependent amplification (HDA), and recombinase polymerase amplification (RPA), have great potential for on-site, point-of-care, and in situ assay applications. These amplification techniques eliminate the need for temperature cycling, as required for the polymerase chain reaction (PCR), while achieving comparable amplification yields. We highlight here recent advances in the exponential amplification reaction (EXPAR) for the detection of nucleic acids, proteins, enzyme activities, cells, and metal ions. The incorporation of fluorescence, colorimetric, chemiluminescence, Raman, and electrochemical approaches enables the highly sensitive detection of a variety of targets. Remaining issues, such as undesirable background amplification resulting from nonspecific template interactions, must be addressed to further improve isothermal and exponential amplification techniques.
Public Key Cryptography for Initial Authentication in Kerberos (PKINIT) (2006)

This document describes protocol extensions (hereafter called PKINIT)
to the Kerberos protocol specification. These extensions provide a
method for integrating public key cryptography into the initial
authentication exchange, by using asymmetric-key signature and/or
encryption algorithms in pre-authentication data fields. [STANDARDS-
TRACK]
Systemic Complement Depletion Inhibits Experimental Cerebral Vasospasm (1996)

The results suggest a role for complement activation in SAH.
Role of the Hemagglutinin-Neuraminidase Protein in the Mechanism of Paramyxovirus-Cell Membrane Fusion (2002)

Paramyxovirus infects cells by initially attaching to a sialic acid-containing cellular receptor and subsequently fusing with the plasma membrane of the cells. Hemagglutinin-neuraminidase (HN) protein, which is responsible for virus attachment, interacts with the fusion protein in a virus type-specific manner to induce efficient membrane fusion. To elucidate the mechanism of HN-promoted membrane fusion, we characterized a series of Newcastle disease virus HN proteins whose surface residues were mutated. Fusion promotion activity was substantially altered in only the HN proteins with a mutation in the first or sixth beta sheet. These regions overlap the large hydrophobic surface of HN; thus, the hydrophobic surface may contain the fusion promotion domain. Furthermore, a comparison of the HN structure crystallized alone or in complex with 2-deoxy-2,3-dehydro-N-acetylneuraminic acid revealed substantial conformational changes in several loops within or near the hydrophobic surface. Our results suggest that the binding of HN protein to the receptor induces the conformational change of residues near the hydrophobic surface of HN protein and that this change triggers the activation of the F protein, which initiates membrane fusion.
Design and Implementation of Practical Step Detection Algorithm for Wrist-worn Devices (2016)

In recent years, interest in wrist-worn devices has been growing, as market of wearable activity tracking devices have been enlarged. But, many wrist-worn devices have three main problems that activity tracking algorithms for wrist-worn devices should overcome: lack of sensor variety due to power consumption, low computing power, and noise from various sensor-carrying modes and walking velocities. This paper discusses an activity tracking, especially regarding step detection algorithm using three-axis accelerometer for wrist-worn devices. The proposed algorithm consists of three phases, which address the problems of wrist-worn devices. The first data preprocessing phase calculates the Euclidean norm of the acceleration vector. It enables the algorithm to track the movement of a device only with the acceleration data. The second data filtering phase reduces the noise with a simple digital low-pass filter. Then, the third peak detection phase adopts a sign-of-slope method and average threshold method to accurately detect the step peaks under different sensor-carrying modes and velocity conditions. A wrist-worn hardware prototype is designed and realized for algorithm evaluation. The experiment results show that the proposed algorithm is superior to the compared existing algorithm and commercial devices. The averaged detection error is approximately 1% in different test conditions.
Neuroprotective Effect of Granulocyte Colony–Stimulating Factor After Focal Cerebral Ischemia (2003)

G-CSF achieved a significant neuroprotective effect in cell culture and after intravenous administration after stroke. Increased STAT3 expression in the penumbra of G-CSF-treated rats suggests mediation by G-CSFR.
Cyclin-Dependent Kinase 2 Functions in Normal DNA Repair and Is a Therapeutic Target in BRCA1-Deficient Cancers (2006)

Abnormal regulation of progression from G(1) to S phase of the cell cycle by altered activity of cyclin-dependent kinases (CDKs) is a hallmark of cancer. However, inhibition of CDKs, particularly CDK2, has not shown selective activity against most cancer cells because the kinase seems to be redundant in control of cell cycle progression. Here, we show a novel role in the DNA damage response and application of CDK inhibitors in checkpoint-deficient cells. CDK2(-/-) mouse fibroblasts and small interfering RNA--mediated or small-molecule--mediated CDK2 inhibition in MCF7 or U2OS cells lead to delayed damage signaling through Chk1, p53, and Rad51. This coincided with reduced DNA repair using the single-cell comet assay and defects observed in both homologous recombination and nonhomologous end-joining in cell-based assays. Furthermore, tumor cells lacking cancer predisposition genes BRCA1 or ATM are 2- to 4-fold more sensitive to CDK inhibitors. These data suggest that inhibitors of CDK2 can be applied to selectively enhance responses of cancer cells to DNA-damaging agents, such as cytotoxic chemotherapy and radiotherapy. Moreover, inhibitors of CDKs may be useful therapeutics in cancers with defects in DNA repair, such as mutations in the familial breast cancer gene BRCA1.
Characterization of a glucose-repressed pyruvate kinase (Pyk2p) in Saccharomyces cerevisiae that is catalytically insensitive to fructose-1,6-bisphosphate (1997)

We have characterized the gene YOR347c of Saccharomyces cerevisiae and shown that it encodes a second functional pyruvate kinase isoenzyme, Pyk2p. Overexpression of the YOR347c/PYK2 gene on a multicopy vector restored growth on glucose of a yeast pyruvate kinase 1 (pyk1) mutant strain and could completely substitute for the PYK1-encoded enzymatic activity. PYK2 gene expression is subject to glucose repression. A pyk2 deletion mutant had no obvious growth phenotypes under various conditions, but the growth defects of a pyk1 pyk2 double-deletion strain were even more pronounced than those of a pyk1 single-mutation strain. Pyk2p is active without fructose-1,6-bisphosphate. However, overexpression of PYK2 during growth on ethanol did not cause any of the deleterious effects expected from a futile cycling between pyruvate and phosphoenolpyruvate. The results indicate that the PYK2-encoded pyruvate kinase may be used under conditions of very low glycolytic flux.
A Clinical Trial of Hypertonic Saline Nasal Spray in Subjects With the Common Cold or Rhinosinusitis (1998)

Hypertonic saline does not improve nasal symptoms or illness duration in patients with the common cold or rhinosinusitis.
Use of fish oil in parenteral nutrition: rationale and reality (2006)

Excessive or inappropriate inflammation and immunosuppression are components of the response to surgery, trauma, injury and infection in some individuals and can lead, progressively, to sepsis and septic shock. The hyperinflammation is characterised by the production of inflammatory cytokines, arachidonic acid-derived eicosanoids and other inflammatory mediators, while the immunosuppression is characterised by impairment of antigen presentation and of T-helper lymphocyte type-1 responses. Long-chain n-3 fatty acids from fish oil decrease the production of inflammatory cytokines and eicosanoids. They act both directly (by replacing arachidonic acid as an eicosanoid substrate and by inhibiting arachidonic acid metabolism) and indirectly (by altering the expression of inflammatory genes through effects on transcription factor activation). Thus, long-chain n-3 fatty acids are potentially useful anti-inflammatory agents and may be of benefit in patients at risk of hyperinflammation and sepsis. As a consequence, an emerging application for n-3 fatty acids, in which they may be added to parenteral (or enteral) formulas, is in surgical or critically-ill patients. Parenteral nutrition that includes n-3 fatty acids appears to preserve immune function better than standard formulas and appears to diminish the extent of the inflammatory response. Studies to date are suggestive of clinical benefits from these approaches, especially in patients post surgery, although evidence of clinical benefit in patients with sepsis is emerging.