gebhart/patrepeval huggingface dataset:
Conserved amino acid networks involved in antibody variable domain interactions (2008)

Engineered antibodies are a large and growing class of protein therapeutics comprising both marketed products and many molecules in clinical trials in various disease indications. We investigated naturally conserved networks of amino acids that support antibody V(H) and V(L) function, with the goal of generating information to assist in the engineering of robust antibody or antibody-like therapeutics. We generated a large and diverse sequence alignment of V-class Ig-folds, of which V(H) and V(L) domains are family members. To identify conserved amino acid networks, covariations between residues at all possible position pairs were quantified as correlation coefficients (phi-values). We provide rosters of the key conserved amino acid pairs in antibody V(H) and V(L) domains, for reference and use by the antibody research community. The majority of the most strongly conserved amino acid pairs in V(H) and V(L) are at or adjacent to the V(H)-V(L) interface suggesting that the ability to heterodimerize is a constraining feature of antibody evolution. For the V(H) domain, but not the V(L) domain, residue pairs at the variable-constant domain interface (V(H)-C(H)1 interface) are also strongly conserved. The same network of conserved V(H) positions involved in interactions with both the V(L) and C(H)1 domains is found in camelid V(HH) domains, which have evolved to lack interactions with V(L) and C(H)1 domains in their mature structures; however, the amino acids at these positions are different, reflecting their different function. Overall, the data describe naturally occurring amino acid networks in antibody Fv regions that can be referenced when designing antibodies or antibody-like fragments with the goal of improving their biophysical properties.
Detection of estrus by visual observation and radiotelemetry in peripubertal, estrus-synchronized beef heifers. (1996)

The effectiveness of two estrus-detection methods (visual observation and radiotelemetric, pressure-sensitive, rump-mounted devices) was compared in peripubertal, crossbred yearling beef heifers. Heifers (n = 50) were fitted with a pressure-sensitive device affixed to their rumps to which a battery-operated radio transmitter was connected. Activation of the sensor sent a radiotelemetric signal to a microcomputer via a fixed radio antenna. Heifer identification, date, time, and duration of standing events were recorded. Estrus was synchronized by feeding melengestrol acetate (MGA) for 14 d and then injecting PGF2 alpha 17 d after the last daily dose of MGA. Following the injection of PGF2 alpha, heifers were observed visually for signs of estrus at 0730 and 1630 (45 min each). Estrus was detected in 41 of 49 heifers (one lost the device) by visual observation and(or) the radiotelemetric device. Number of standing events during estrus, determined by the radiotelemetric device, averaged 50.1 +/- 6.4 per heifer, with the duration of estrus ranging from 2.6 to 26.2 h (average = 14 +/- .8 h). Visual observation failed to detect 11 of 41 heifers (37%) that were detected by the radiotelemetric device. Heifers with fewer standing events (19.3 vs 60.5; P < .001) and estrus of shorter duration (8.4 vs 15.6 h; P < .001) were those not identified by visual observation. Based on intervals between the first detected standing event of estrus and time of insemination, a wide window of fertility seems to exist in some heifers. Radiotelemetric devices were useful in identifying a greater (P < .05) proportion (100%) of heifers in estrus (increased efficiency) compared with visual observation (73%). However, accuracy of both methods was similar.
Multi-Layer Self-Organizing Semantic Maps (1993)

Self-organizing multi-layer semantic maps are proposed and simulated. The semantic maps proposed by H. Ritter and T. Kohonen have a feature that the semantic relations in the input data are reflected by their relative distances in the maps. They consist of minimal two layers. Since the proposed maps are multi-layer type, they can do higher level information processing compared with the conventional minimal two-layer semantic maps. The computer simulation results indicate the effectiveness of the proposed maps: the maps can do hierarchical self-classification both in self-organizing symbol map and in role-based semantic map.
The Isolation and Characterization in Yeast of a Gene for ArabidopsisS-Adenosylmethionine:Phospho-EthanolamineN-Methyltransferase (2000)

Saccharomyces cerevisiae opi3 mutant strains do not have the phospholipid N-methyltransferase that catalyzes the two terminal methylations in the phosphatidylcholine (PC) biosynthetic pathway. This results in a build up of the intermediate phosphatidylmonomethylethanolamine, causing a temperature-sensitive growth phenotype. An Arabidopsis cDNA library was used to isolate three overlapping plasmids that complemented the temperature-sensitive phenotype. Phospholipid analysis showed that the presence of the cloned cDNA caused a 65-fold reduction in the level of phosphatidylmonomethylethanolamine and a significant, though not equivalent, increase in the production of PC. Sequence analysis established that the cDNA was not homologous to OPI3 or to CHO2, the only other yeast phospholipid N-methyltransferase, but was similar to several other classes of methyltransferases. S-adenosyl-Met:phospho-base N-methyltransferase assays revealed that the cDNA catalyzed the three sequential methylations of phospho-ethanolamine to form phospho-choline. Phospho-choline is converted to PC by the CDP-choline pathway, explaining the phenotype conferred upon the yeast mutant strain by the cDNA. In accordance with this the gene has been named AtNMT1. The identification of this enzyme and the failure to isolate a plant phospholipid N-methyltransferase suggests that there are fundamental differences between the pathways utilized by yeast and by some plants for synthesis of PC.
Non-equilibrium freezing behaviour of aqueous systems (1977)

The tendencies to non-equilibrium freezing behaviour commonly noted in representative aqueous systems derive from bulk and surface properties according to the circumstances. Supercooling and supersaturation are limited by heterogeneous nucleation in the presence of solid impurities. Homogeneous nucleation has been observed in aqueous systems freed from interfering solids. Once initiated, crystal growth is ofter slowed and, very frequently, terminated with increasing viscosity. Nor does ice first formed always succeed in assuming its most stable crystalline form. Many of the more significant measurements on a given systeatter permitting the simultaneous representation of thermodynamic and non-equilibrium properties. The diagram incorporated equilibrium melting points, heterogeneous nucleation temperatures, homogeneous nucleation temperatures, glass transition and devitrification temperatures, recrystallization temperatures, and, where appropriate, solute solubilities and eutectic temperatures. Taken together, the findings on modle systems aid the identification of the kinetic and thermodynamic factors responsible for the freezing-thawing survival of living cells.
Tumour-Endothelial Cell Communications: Important and Indispensable Mediators of Tumour Angiogenesis. (2016)

Angiogenesis is an essential aspect of tumour growth and metastasis. Solid tumours cannot grow beyond 2-3 mm in diameter without inducing the formation of new blood vessels to support the energetic requirements of tumour cells. Angiogenesis is stimulated by cancer cells through a wide variety of cell-to-cell communication means. Cancer cells can induce endothelial changes by directly targeting cells via soluble factors, adhesion receptors, gap junctions and vesicles. They also can stimulate endothelial signaling pathways in an indirect way, e.g. by activating stromal cells, by secreting proteases into the extracellular space or even by changing the pH, temperature and availability of oxygen and nutrients. Anti-angiogenic drugs appear to be an effective cancer treatment in animal models but have been shown to have a limited effect in the long term. Resistance to anti-angiogenic therapies has been attributed to the ability of cancer cells to induce angiogenesis in a different way. We propose that cancer cells also change the way they communicate with endothelial cells in order to escape therapies that inhibit angiogenesis and that a better knowledge of this phenomenon will help us design more efficient drugs.
Forces acting on a small particle in an acoustical field in a viscous fluid (2012)

We calculate the acoustic radiation force from an ultrasound wave on a compressible, spherical particle suspended in a viscous fluid. Using Prandtl-Schlichting boundary-layer theory, we include the kinematic viscosity of the solvent and derive an analytical expression for the resulting radiation force, which is valid for any particle radius and boundary-layer thickness provided that both of these length scales are much smaller than the wavelength of the ultrasound wave (millimeters in water at megahertz frequencies). The acoustophoretic response of suspended microparticles is predicted and analyzed using parameter values typically employed in microchannel acoustophoresis.
University Medical Information Network - Past, Present, and Future (1998)

The University Medical Information Network (UMIN), established in 1989, is a network service organization for national university hospitals in Japan. It has provided various medical information services to medical professionals, including database, electronic mail, and news services. Although its initial network was constructed as a closed network using N1 protocol, it now adopts TCP/IP protocol and is open to other medical professionals via the Internet. The next UMIN network system is planned to be constructed as a secure virtual closed network on the Internet, using cipher technology, and to provide secure information services to national university hospitals via the closed network, and to other medical professional via the Internet. User friendly interface and flexible system development were made possible by adopting TCP/IP, and the number of users dramatically increased accordingly. However, the database, software design, and human organizations developed in the N1 era have now proven to be of great value, and contribute to todayís flourishing state of the UMIN.
Cloning of a human cDNA encoding a novel enzyme involved in the elongation of long-chain polyunsaturated fatty acids (2000)

The Saccharomyces cerevisiae protein ELO2p is involved in the elongation of saturated and monounsaturated fatty acids. Among several sequences with limited identity with the S. cerevisiae ELO2 gene, a consensus cDNA sequence was identified from the LifeSeq(R) database of Incyte Pharmaceuticals, Inc. Human liver cDNA was amplified by PCR using oligonucleotides complementary to the 5' and 3' ends of the putative human cDNA sequence. The resulting full-length sequence, termed HELO1, consisted of 897 bp, which encoded 299 amino acids. However, in contrast with the ELO2 gene, expression of this open reading frame in S. cerevisiae demonstrated that the encoded protein was involved in the elongation of long-chain polyunsaturated fatty acids, as determined by the conversion of gamma-linolenic acid (C(18:3, n-6)) into dihomo-gamma-linolenic acid (C(20:3, n-6)), arachidonic acid (C(20:4, n-6)) into adrenic acid (C(22:4, n-6)), stearidonic acid (C(18:4, n-3)) into eicosatetraenoic acid (C(20:4, n-3)), eicosapentaenoic acid (C(20:5, n-3)) into omega3-docosapentaenoic acid (C(22:5, n-3)) and alpha-linolenic acid (C(18:3, n-3)) into omega3-eicosatrienoic acid (C(20:3, n-3)). The predicted amino acid sequence of the open reading frame had only 29% identity with the yeast ELO2 sequence, contained a single histidine-rich domain and had six transmembrane-spanning regions, as suggested by hydropathy analysis. The tissue expression profile revealed that the HELO1 gene is highly expressed in the adrenal gland and testis. Furthermore, the HELO1 gene is located on chromosome 6, best known for encoding the major histocompatibility complex, which is essential to the human immune response.
The functional gastrointestinal disorders and the Rome II process (1999)

The functional gastrointestinal disorders and the Rome II process
Osteopontin Is a Strong Predictor of Incipient Diabetic Nephropathy, Cardiovascular Disease, and All-Cause Mortality in Patients With Type 1 Diabetes (2014)

Serum OPN is a strong predictor of incipient diabetic nephropathy, a first-ever CVD event, and all-cause mortality in patients with T1D. Serum OPN may be of clinical significance for the risk prediction of CVD events in patients with T1D.
Depression in association with severe obesity: changes with weight loss. (2003)

Severely obese subjects, especially younger women with poor body image, are at high risk for depression. We found sustained improvement with weight loss. These findings also support the hypothesis that severe obesity causes or aggravates depression.
AN EXTENSION OF THE51Cr-RELEASE ASSAY FOR THE ESTIMATION OF MOUSE CYTOTOXINS (1968)

SUMMARY The 51Cr-release assay for measurement of cytotoxic reactions, with its many advantages, has hitherto been applicable only to mouse cell types which occur free from contamination with erythrocytes. A simple method is presented which can selectively lyse contaminating erythrocytes from tissue cell preparations without damaging the tissue cells. The tissue cells can then be labelled and tested by the 51Cr-release cytotoxicity assay. The usefulness of the method is shown by demonstrating its success with suspensions of mouse spleen cells and with a hemorrhagic ascites sarcoma.
High-fidelity gene targeting in embryonic stem cells by using sequence replacement vectors. (1992)

Mutations were targeted to the Hprt locus in murine embryonic stem cells by using sequence replacement vectors. When the vector was designed such that the mutated sequences were flanked on both sides by several kilobases of DNA homologous to the target locus, replacement of chromosomal sequences with the exogenous DNA occurred with precision. If, on the other hand, the target-homologous DNA on one arm of the vector was reduced to below 1 kb in length, the fidelity of recombination was diminished.
American Ginseng Berry Juice Intake Reduces Blood Glucose and Body Weight in ob / ob Mice (2007)

Diabetes is a serious chronic metabolic disease and has a significant impact on patients' lives and the health care system. We previously observed that the organic solvent extract of American ginseng berry possessed significant antidiabetic effects in obese diabetic ob/ob mice after intraperitoneal injection. If American ginseng berry is useful as a dietary supplement, simple preparation and oral intake would be a convenient, safe, and practical means for consumers. In this study, the simply prepared berry juice was first analyzed using high-performance liquid chromatography, and then administered orally in the ob/ob mice. The animals received daily berry juice 0.6 mL/kg or vehicle for 10 consecutive days. The results indicated that oral juice administration significantly lowered fasting blood glucose levels, and this effect continued for at least 10 d after cessation of the treatment. Data from intraperitoneal glucose tolerance test demonstrated that there was a notable improvement in glucose tolerance in the juice treated group. In addition, the berry juice significantly reduced body weight. Our data suggest that ginseng berry juice, as a dietary supplement, may have functional efficacy in consumers with diabetes.
La ciudad en el tiempo (notas sobre la poesía de Jaime Gil de Biedma) (1986)

A new species of the genus Metopolophium Mordvilko, 1914 (Hemiptera: Aphididae: Aphidinae: Macrosiphini) is described and illustrated. Apterous and alate viviparous females, oviparous females, and apterous males of Metopolophium rogeri sp. nov. on Rosa beggeriana (Rosaceae) are collected from Kerman Province, Iran. The new species is morphologically most similar to M. alpinum Hille Ris Lambers, 1966, but is characterized by the low ratio of processus terminalis to basal segment of antennal segment VI, high ratio of siphunculus to cauda length and the presence of many more accessory setae on the ultimate rostral segment. This holocyclic aphid is monoecious and not attended by ants. The biometric data are given, and the key to the aphids associated with Rosa species in Blackman and Eastop (2021) is modified to accommodate the new species.
Recurrent Spatial Transformer Networks (2015)

We integrate the recently proposed spatial transformer network (SPN) [Jaderberg et. al 2015] into a recurrent neural network (RNN) to form an RNN-SPN model. We use the RNN-SPN to classify digits in cluttered MNIST sequences. The proposed model achieves a single digit error of 1.5% compared to 2.9% for a convolutional networks and 2.0% for convolutional networks with SPN layers. The SPN outputs a zoomed, rotated and skewed version of the input image. We investigate different down-sampling factors (ratio of pixel in input and output) for the SPN and show that the RNN-SPN model is able to down-sample the input images without deteriorating performance. The down-sampling in RNN-SPN can be thought of as adaptive down-sampling that minimizes the information loss in the regions of interest. We attribute the superior performance of the RNN-SPN to the fact that it can attend to a sequence of regions of interest.
The presence of nuclear and mitochondrial uracil-DNA glycosylase in extracts of human KB cells. (1980)

Extracts of human KB cells contain detectable uracil-DNA glycosylase activity. The majority of the activity is located within the nuclear fraction, however we present evidence for the presence of identifiable uracil-DNA glycosylase activity associated with the mitochondrial fraction of these cells.
Finite size effect on hydrogen gas sensing performance in single Pd nanowires (2008)

We present the hydrogen sensing performance of individual Pd nanowires grown by electrodeposition into nanochannels of anodized aluminum oxide (AAO) templates investigated as a function of the nanowire diameter. Four-terminal devices based on individual Pd nanowires were found to successfully detect hydrogen gas (H(2)). Our experimental results show that the H(2) sensing sensitivity increases and the response time decreases with decreasing diameter of Pd nanowires with d = 400, 200, 80 and 20 nm, due to the high surface-to-volume ratio and short diffusion paths, respectively. This is in qualitatively good agreement with simulated results obtained from a theoretical model based on a combination of the rate equation and diffusion equation.
Strategies and Implications for Network Participation in Regional Climate and Energy Planning (2013)

Regional climate and energy planning in Sweden has long been fairly weak. Starting in 2008, however, the regional administrative level was strengthened, when the County Administrative Boards (CABs) were commissioned to develop regional climate and energy strategies. Coordinating and involving various stakeholders in the strategy work was essential to the assignment. The process of developing these strategies is the present focus. The paper analyses CAB's use of various participation approaches when establishing networks, in order to examine how these strategies have influenced the implementation of regional climate and energy strategies and, consequently, the realization of their goals. From case studies of four Swedish counties, we conclude that different network participation approaches result in different implementation outcomes. A meta-governor using a policy participation strategy when establishing networks facilitates implementation, while a meta-governor using deliberative or learning strategies for network participation has few opportunities for implementation.
<title>Novel architecture for high-speed dual-image generation of pattern data for phase-shifting reticle inspection</title> (1992)

The pattern data representing ULSI photolithography layers continues to grow exponentially when viewed at the image plane. Data derivation, verification, conversion, and movement have resulted in significant logistical problems and reticle production bottlenecks even with current device densities and reticle manufacturing technologies. With the advent of phase shifting reticle manufacturing and even more dense ULSI devices, database image generation for reticle defect inspection becomes an even more serious issue. Examination of 64 MBit pattern characteristics show that total figure counts per layer approach 1 billion figures per layer. Phase shifting structures increase figure counts per layer to over 1 billion figures. Defect sensitivities of 0.40 micrometers for chrome defects and 0.30 micrometers for phase shift defects are required for 64 MBit reticle inspection. Single die inspection area exceeds 5000 mm2 and die pixel counts are over 1011 pixels. Current reticle inspection database image generation technology requires ten hours per inspection pass. Data load times exceed one hour and data conversion to the inspection format exceeds ten hours. Total reticle inspection time in the manufacturing environment may approach 40 hours. A novel pattern generator architecture allowing 64 MBit reticle inspection in one hour is proposed. The NPG architecture includes a new data format, an integrated data conversion package, and a high resolution, high speed image generator. NPG data conversion performance is analyzed and 782 million figure 64 MBit data conversions are performed in less than one minute. Resulting file sizes are one million bytes. The NPG data format is shown to allow increased edge placement resolution to support increased inspection sensitivity. A method for simultaneously generating chrome and phase shift images is presented.
AMYLOIDOSIS: A REVIEW OF RECENT DIAGNOSTIC AND THERAPEUTIC DEVELOPMENTS (1997)

Amyloid deposition is associated with a diverse range of disorders that includes Alzheimer's disease, type II diabetes mellitus and dialysis arthropathy. Although less common, systemic AA and AL amyloidosis remain important because effective treatments have increasingly become available. The pathology in all forms of amyloidosis involves the extracellular deposition of protein as characteristic fibrillar aggregates which interfere with tissue structure and function. Amyloid fibrils are derived from different unrelated proteins in the different forms of the disease but share many common properties, including the capacity to bind the normal plasma protein serum amyloid P component (SAP). This is the basis for our development of radiolabelled SAP as a nuclear medicine tracer for the diagnosis and quantitative monitoring of amyloid. Serial studies have shown that the deposits are far from inert but are actually turned over quite rapidly in many patients. The treatment of amyloidosis involves supportive measures whilst every effort is made to reduce the supply of the respective fibril precursor protein. Under favourable circumstances further amyloid deposition will be prevented. existing deposits will regress and improvement of organ function will occur. Since this strategy is not always possible or may fail, new approaches to inhibit fibril formation and promote regression of amyloid are being pursued.
Complementary silicide source/drain thin-body MOSFETs for the 20 nm gate length regime (2002)

Thin-body transistors with silicide source/drains were fabricated with gate-lengths down to 15 nm. Complementary low-barrier silicides were used to reduce contact and series resistance. Minimum gate-length transistors with T/sub ox/=40 /spl Aring/ show PMOS |I/sub dsat/|=270 /spl mu/A//spl mu/m and NMOS |I/sub dsat/|=190 /spl mu/A//spl mu/m with V/sub ds/=1.5 V, |V/sub g/-V/sub t/|=1.2 V and, I/sub on//I/sub off/>10/sup 4/. A simple transmission model, fitted to experimental data, is used to investigate effects of oxide scaling and extension doping.