gebhart/patrepeval huggingface dataset:
Improved Parameters for the Martini Coarse-Grained Protein Force Field (2012)

The Martini coarse-grained force field has been successfully used for simulating a wide range of (bio)molecular systems. Recent progress in our ability to test the model against fully atomistic force fields, however, has revealed some shortcomings. Most notable, phenylalanine and proline were too hydrophobic, and dimers formed by polar residues in apolar solvents did not bind strongly enough. Here, we reparametrize these residues either through reassignment of particle types or by introducing embedded charges. The new parameters are tested with respect to partitioning across a lipid bilayer, membrane binding of Wimley-White peptides, and dimerization free energy in solvents of different polarity. In addition, we improve some of the bonded terms in the Martini protein force field that lead to a more realistic length of α-helices and to improved numerical stability for polyalanine and glycine repeats. The new parameter set is denoted Martini version 2.2.
Synthesis, Antimicrobial Evaluation, and Docking Studies of Novel 4‐Substituted Quinazoline Derivatives as DNA‐Gyrase Inhibitors (2010)

Quinazoline derivatives are reported to have anti-inflammatory, analgesic, antibacterial, and anticancer activities. The incorporation of "OCH₂CONH₂" (oxymethylcarbamide) at 4th position of the quinazoline ring was found to influence the biological activities of the molecules. With this rationale, some new oxadiazolyl methyloxy quinazolines, pyrazolyl acetoxy methyl quinazolines, triazolylmethyloxy quinazolines were synthesized from anthranilic acid through quinazolyl oxyacetylhydrazide intermediates. All the compounds were characterized by IR, ¹H-NMR, EI-MS, and C, H, N analyses and evaluated for their antimicrobial activity. Docking studies on the DNA-gyrase enzyme (1KZN) show their role in the antimicrobial activity of the molecules and explain the higher potency of compounds 6a, 6b, 8a, 8b based on ReRanking scores and binding poses of the molecules.
A body sensor network for tracking and monitoring of functional arm motion (2009)

In this paper, we present a novel sensing technique, optical linear encoder (OLE), in which the motion of an optical encoder on a reflective strip is converted to limb joints' goniometric data. A body sensing module is designed to integrate the OLE and an accelerometer. A sensor network of three sensing modules is established via Controller Areas Network (CAN) bus to capture full motion of human arm with a 7-DOF kinematic model. In addition, a statistical study was conducted to confirm the repeatability and reliability of our sensor network. Results demonstrate that the sensor system has strong potential to be used as a low-cost tool for motion capture, and objective arm function evaluation for both short-term and long-term monitoring.
The effect of gastrodin on expression of apoptosis and Tyrosine hydroxylase neurons in substantia nigra pars compacta in rats of Parkinson' s disease (2011)

Objective To investigate the etiopathogenesis of Parkinson' s disease (PD) and the mechanism of action of the gastrodin in order to prevent and cure PD. Methods Male Wistar rats were left-striatum injected with 6-OHDA (20 μg) to establish PD model. To observe the effect of gastrodin on the expression of Tyrosine hydroxylase positive (TH +) and Caspase-3 positive (Caspase-3 +) neurons in substantia nigra pars compacta (SNpc) and ventral tegmental area (VTA) by immunohistochemistry technique. Results There were statistically significant differences in the levels of TH + neurons in SNpc and VTA in rats of PD disease between groups (F = 13.29,5.04, P ＜0.01). To compared with normal group[(32.13 ±4.84), (30.23 ± 3.21)], the levels of TH + neurons in SNpc and VTA in rats in model group (18.89 ± 3.73,24.20 ± 6.35) were significantly decreased (P ＜ 0.01),the loss of TH + neurons declined after treatment with gastrodin or madopar, the levels of TH + neurons in SNpc and VTA in rats in small dose group[(26. 24 ± 3.06), (26.31 ± 6. 1)], in middle dose group[(22.4 ± 3.81),(26.91 ±6.28)], in large dose group[(20.95 ±4.71),(27.3 ±7.1)]and in madopar group[(27.89 ±4. 56), (25.97 ±5.14)]were obviously increased, the levels of TH + neurons in SNpc in rats in small dose group and in madopar group were significantly increased (P ＜ 0.05). There were statistically significant differences in the levels of Caspase-3 + neurons in SNpc and VTA of rats of PD disease between groups (F = 6. 09,5. 53, P ＜ 0. 01).To compared with normal group[(9.83 ± 3.03), (7.04 ± 1.76)], the levels of Caspase-3 + neurons in SNpc and VTA in rats in model group[(14.53 ± 2.33), (12.84 ± 2.58)]were significantly increased (P ＜ 0.01), the levels of Caspase-3 .+ neurons in SNpc and VTA in rats in small dose group[(10.68 ± 1.83), (7.72 ± 1.92)], in middle dose group[(11.29 ± 2.8), (10.38 ± 3.79)], in large dose group[(11.89 ± 2.97), (11.37 ± 1.86)]and in madopar group[(9.99 ± 3.3), (10.69 ± 3.11)]were obviously decreased, the levels of Caspase-3 + neurons in SNpc in madopar group and in VTA in small dose group were significantly decreased (P ＜ 0.05). The trend of change of TH + neurons is opposite to that of Caspase-3 + neurons in gastrodin or madopar treatment groups. Conclusion Gastrodin may suppress the loss and apoptosis in SNpc by adjusting Caspase-3. The effect of small dose group is better,suggesting gastrodin can have different neuroprotection on dopamine neuron.

Key words: 
Gastrodin ; 6-hydroxydopamine(6-OHDA) ;  Rats;  Apoptosis; Tyrosine hydroxylase
Heterogeneous parallel computing: from clusters of workstations to hierarchical hybrid platforms (2014)

The paper overviews the state of the art in design and implementation of data parallelscientic applications on heterogeneous platforms. It covers both traditional approaches originallydesigned for clusters of heterogeneous workstations and the most recent methods developed in thecontext of modern multicore and multi-accelerator heterogeneous platforms.
Efficient induction of antitumor T cell immunity by exosomes derived from heat‐shocked lymphoma cells (2006)

Exosomes secreted by tumor cells could serve as a promising immunotherapeutic tumor vaccine. Heat shock proteins (HSP) induced in tumor cells by heat shock are molecular chaperones with potent adjuvant activity in the induction of antigen-specific T cell responses. To improve exosome-based tumor vaccines, we have investigated the efficacy of exosomes derived from heat-shocked mouse B lymphoma cells (HS-Exo) in the induction of antitumor immune responses. We found that HS-Exo, compared with control exosomes derived from the same cells (Exo), contain more HSP60 and HSP90 and increased amounts of molecules involved in immunogenicity including MHC class I, MHC class II, CD40, CD86, RANTES and IL-1beta. Furthermore, HS-Exo induce both phenotypic and functional maturation of dendritic cells more efficiently. HS-Exo immunization activates T cell responses more potently. Importantly, HS-Exo induce dramatically increased antitumor immune responses compared to control exosomes from the same cells in prophylaxis and therapeutic in vivo lymphoma models. We further demonstrate that CD8(+) T cells are the predominant T cell subset responsible for the antitumor effect of HS-Exo and that CD4(+) T cells are necessary in the induction phase of tumor rejection in a prophylaxis model. These findings provide a novel strategy to improve the efficacy of exosome-based tumor vaccines.
Absolute quantification of brain metabolites by proton magnetic resonance spectroscopy in normal-appearing white matter of multiple sclerosis patients (1999)

The aim of this research was to obtain an absolute quantification of the N-acetyl-aspartate, choline, creatine and phosphocreatine levels in normal-appearing white matter by means of 1H magnetic resonance spectroscopy in a group of multiple sclerosis patients (27 with the relapsing-remitting form and 13 with the secondary progressive form). These values were compared with those of a group of 12 age-matched healthy control subjects. A significant decrease in the N-acetyl-aspartate concentration was found in normal-appearing white matter of frontal and parietal brain areas in multiple sclerosis patients compared with the same areas in control subjects. This reduction was more evident in progressive patients. The decrease in the N-acetyl-aspartate concentration in normal-appearing white matter significantly correlated with the Expanded Disability Status and the lesional load. No significant change was found in the concentration of creatine or choline. This finding concurs with previous evidence of heterogeneity in the multiple sclerosis pathological process which is not confined to the lesions and involves not only myelin, but also axons, even in white matter which appears normal on MRI.
Breast compression in mammography: How much is enough? (2003)

The amount of breast compression that is applied during mammography potentially influences image quality and the discomfort experienced. The aim of this study was to determine the relationship between applied compression force, breast thickness, reported discomfort and image quality. Participants were women attending routine breast screening by mammography at BreastScreen New South Wales Central and Eastern Sydney. During the mammographic procedure, an 'extra' craniocaudal (CC) film was taken at a reduced level of compression ranging from 10 to 30 Newtons. Breast thickness measurements were recorded for both the normal and the extra CC film. Details of discomfort experienced, cup size, menstrual status, existing breast pain and breast problems were also recorded. Radiologists were asked to compare the image quality of the normal and manipulated film. The results indicated that 24% of women did not experience a difference in thickness when the compression was reduced. This is an important new finding because the aim of breast compression is to reduce breast thickness. If breast thickness is not reduced when compression force is applied then discomfort is increased with no benefit in image quality. This has implications for mammographic practice when determining how much breast compression is sufficient. Radiologists found a decrease in contrast resolution within the fatty area of the breast between the normal and the extra CC film, confirming a decrease in image quality due to insufficient applied compression force.
A real-time distributed computer system for coordinated-motion control of two industrial robots (2005)

The design of a distributed computer system for coordinated-motion control of two industrial robots is discussed. The control mechanism for the coordinated-motion control has a hierarchical nature. For hierarchically related computational tasks, a tree-structured multicomputer system is selected as the architecture of the distributed computer system (DCS). The emphasis of the work is on the design of a distributed operating system (DOS) called REKCOR, which stands for REal-time Kernel for Coordinating Robots. It provides transparent operations to the users, and maintains the flexibility and modularity of the system. The successful design of REKCOR is verified by a practical experiment, in which the distributed computer system controls two industrial robots to successfully execute a coordinated-motion.
The Effect of Potassium and Bicarbonate Ions on the Rise in Blood Pressure Caused by Sodium Chloride (1982)

1. A group of eight patients with mild hypertension, sensitive to sodium intake, were studied. 2. Sodium chloride (70 mmol daily) caused their blood pressure to rise by 19/14 mmHg. 3. Sodium bicarbonate (70 mmol daily) caused their blood pressure to rise by 12/5 mmHg. 4. Sodium chloride given together with potassium chloride (70 mmol of each daily) caused their blood pressure to rise by 9.6 mmHg. 5. These results suggest that sodium bicarbonate causes a smaller rise in blood pressure than sodium chloride does and that potassium chloride reduces the blood pressure raising effect of sodium chloride. 6. A low sodium, high potassium and an alkaline diet may therefore be a more effective dietary method to reduce blood pressure than a diet low in sodium alone.
Heat shock proteins in neurodegenerative disorders and aging (2014)

Many members of the heat shock protein family act in unison to refold or degrade misfolded proteins. Some heat shock proteins also directly interfere with apoptosis. These homeostatic functions are especially important in proteinopathic neurodegenerative diseases, in which specific proteins misfold, aggregate, and kill cells through proteotoxic stress. Heat shock protein levels may be increased or decreased in these disorders, with the direction of the response depending on the individual heat shock protein, the disease, cell type, and brain region. Aging is also associated with an accrual of proteotoxic stress and modulates expression of several heat shock proteins. We speculate that the increase in some heat shock proteins in neurodegenerative conditions may be partly responsible for the slow progression of these disorders, whereas the increase in some heat shock proteins with aging may help delay senescence. The protective nature of many heat shock proteins in experimental models of neurodegeneration supports these hypotheses. Furthermore, some heat shock proteins appear to be expressed at higher levels in longer-lived species. However, increases in heat shock proteins may be insufficient to override overwhelming proteotoxic stress or reverse the course of these conditions, because the expression of several other heat shock proteins and endogenous defense systems is lowered. In this review we describe a number of stress-induced changes in heat shock proteins as a function of age and neurodegenerative pathology, with an emphasis on the heat shock protein 70 (Hsp70) family and the two most common proteinopathic disorders of the brain, Alzheimer's and Parkinson's disease.
Improving the performance of the in-band byte stream file transfer XMPP extension (2009)

In looking at the XMPP protocol as an alternative to the ordinary way of transferring files within a health network setting, namely e-mail, performance and security are important factors to consider. For security reasons we preferred to use in-band over out-of-band file transfer. The tradeoff is that this method puts a higher strain on the XMPP server and is significantly slower than its counterpart, out-of-band. In researching a specific XMPP implementation, the Openfire XMPP server, and looking into how it deals with in-band file transfers, we have found some ways to increase in-band file transfer performance, but not in the originally intended way, which would be through improvements in the Openfire source code concerning in-band file transfers.
Mitosis in the Rat Uterus during the Estrous Cycle, Early Pregnancy, and Early Pseudopregnancy (1974)

Mitotic activity was assessed in the endometrium and myometrium of the rat uterus during the estrous cycle, early pregnancy, and electrically induced pseudopregnancy. At proestrus there was pronounced proliferation in the luminal epithelium, the stroma, and in the myometrium. Glandular proliferation occurred only during diestrus. During progestation, epithelial proliferation occurred on the first 2 days of diestrus and then ceased, while stromal mitosis began about 70 h after ovulation, reached maximal intensity during the 4th day of pregnancy or pseudopregnancy, and subsided gradually thereafter. A resurgence of mitotic activity began only in the vicinity of the implanting blastocyst late on Day 5 of pregnancy. Myometrial proliferation also occurred during progestation, on Days 4 and 5. The occurrence of mitosis in the stroma during the estrous cycle indicates that the cyclic corpus luteum secretes functionally significant amounts of progesterone.
A purple barium copper silicate pigment from early China (1992)

AbstractA purple barium copper silicate, BaCuSi206, an artificial inorganic pigment, has been identified, sometimes mixed with the known blue barium copper silicate, BaCuSi4O10. It occurs on- painted objects and in octagonal sticks from China attributed to the Han dynasty (208 Be-AD 220). This man-made pigment, for which the name Han purple is proposed, has not been previously characterized.
Influence of Dietary Protein, Fat or Amino Acids on the Response of Weanling Swine to Aflatoxin B (1989)

Two experiments were conducted using corn from clean or aflatoxin B1 (AFB1)-contaminated (182 ppb) sources. Weanling pigs (28 d) were fed one of eight dietary treatments arranged in a 2 x 2 x 2 factorial design. In Exp. 1 (192 pigs), treatments varied in corn source (clean or AFB1-contaminated), CP level (18 or 20%) and added fat (0 or 5%). At the end of the 28-d growth trials, plasma samples were obtained. An AFB1 x CP level interaction was detected (P less than .05) for growth rate (ADG), feed intake (FI) and feed/gain ratio (F/G). Feeding AFB1 reduced (P less than .05) ADG (.30 vs .37 kg/d) and FI (.57 vs .66 kg/d) and increased F/G (1.88 vs 1.78) of pigs fed 18% CP diets. Performance of pigs fed 20% CP diets was not altered by AFB1. Adding 5% fat to diets improved (P less than .05) F/G but did not improve ADG of pigs fed AFB1. There was an AFB1 x CP x fat interaction (P less than .05) for plasma cholesterol. Adding fat or increasing the CP level prevented the depression of plasma cholesterol in pigs fed AFB1. In Exp. 2 (96 pigs), all diets contained 18% CP and the treatments varied in corn source (clean or AFB1-contaminated), added L-lysine HCl (0 or .25%) and added DL-methionine (0 or .15%). Feeding AFB1 reduced (P less than .05) ADG of pigs fed the 18% CP diet (.44 vs .50 kg/d) but not of pigs fed diets supplemented with .25% lysine.(ABSTRACT TRUNCATED AT 250 WORDS)
The emerging field of ecogenetics. (2000)

Genetic differences in biotransformation enzymes and in target proteins can affect the individual susceptibility to drugs and environmental chemicals. The field of ecogenetics has emerged from the older area of pharmacogenetics, and investigates how genetic polymorphisms may represent risk factors for a number of diseases associated with exposure to toxic chemicals. Here, two polymorphisms, aldehyde dehydrogenase and delta-aminolevulinic acid dehydratase, are briefly discussed in relationship to alcohol and lead toxicity, respectively. The role of genetic polymorphisms in neurodegenerative diseases, such as Parkinson's disease, is also discussed. Furthermore, issues related to the functional significance of genetic polymorphisms, their interaction/combination, and ethical and societal considerations, are briefly addressed.
Analysis of throughput and efficient block size based polling scheme for IEEE 802.11e wireless LANs (2005)

In the recent draft of the 802.11e MAC, the hybrid coordinator (HC) gives transmission opportunity (TXOP) for a station to transmit burst frames in TXOP for improving throughput efficiency. In this paper, we express the expected throughput for the block ack policy in polled TXOP as a closed form function of the number of burst MSDUs, the number of fragmented MPDUs, the data payload length, the frame retry count, the wireless channel condition, and the selected PHY mode. Based on our simulation study and analysis, we show that the TXOP and proper ack policy can enhance system performance, and that there is a block ack efficient block size and frame length to transmit the burst frames for each PHY mode. Moreover, we also show that when the block ack mechanism is combined with link adaptation, it has better throughput performance. Based on the condition of the efficient block ack mechanism, we propose a block size based polling scheme.
A Novel Three-Point Modulation Technique for Fractional-N Frequency Synthesizer Applications (2013)

This paper presents a novel three-point modulation technique for fractional-N frequency synthesizer applications. Convention modulated fractional-N frequency synthesizers suffer from quantization noise, which degrades not only the phase noise performance but also the modulation quality. To solve this problem, this work proposes a three-point modulation technique, which not only cancels the quantization noise, but also markedly boosts the channel switching speed. Measurements reveal that the implemented 2.4 GHz fractional-N frequency synthesizer using three-point modulation can achieve a 2.5 Mbps GFSK data rate with an FSK error rate of only 1.4 %. The phase noise is approximately -98 dBc/Hz at a frequency offset of 100 kHz. The channel switching time is only 1.1 μs with a frequency step of 80 MHz. Comparing with conventional two-point modulation, the proposed three-point modulation greatly improves the FSK error rate, phase noise and channel switching time by about 10 %, 30 dB and 126 μs, respectively.
The Dancing Jew and Other Characters: Art in the Jewish Settlement in Palestine During the 1920s (2002)

(2002). The Dancing Jew and Other Characters: Art in the Jewish Settlement in Palestine During the 1920s. Journal of Modern Jewish Studies: Vol. 1, No. 1, pp. 73-89.
An update of the classical Bokhman’s dualistic model of endometrial cancer (2016)

According to the classical dualistic model introduced by Bokhman in 1983, endometrial cancer (EC) is divided into two basic types. The prototypical histological type for type I and type II of EC is endometrioid carcinoma and serous carcinoma, respectively. The traditional classification is based on clinical, endocrine and histopathological features, however, it sometimes does not reflect the full heterogeneity of EC. New molecular evidence, supported by clinical diversity of the cancer, indicates that the classical dualistic model is valid only to some extent. The review updates a mutational diversity of EC, introducing a new molecular classification of the tumour in regard to data presented by The Cancer Genome Atlas Research Network (TGCA).
Capture of Neutrons by Atoms in a Crystal (1939)

The precise determination of the properties of nuclear resonance levels from the capture of slow neutrons is made difficult by the fact that most of the substances used for absorbers and detectors are in the solid state, so that the calculations of Bethe and Placzek for the influence of the Doppler effect are inapplicable, since these were based on the assumption of a perfect gas. In this paper, their calculations are generalized to include the effect of the lattice binding. Under the assumption that the crystal may be treated as a Debye continuum, it is shown that for sufficiently weak lattice binding, the absorption curve has the same form as it would in a gas, not at the temperature $T$ of the crystal, however, but at a temperature which corresponds to the average energy per vibrational degree of freedom of the lattice (including zero-point energy). In cases of somewhat stronger lattice binding, the line form is found to be more complicated, and may even have a fine structure. Plots are given of the absorption line in several typical cases. An approximate formula for the cross section for self-indication is also derived.
Synthesis of Methyl <i>N</i>-Phenyl Carbamate from Aniline and Dimethyl Carbonate over Supported Zirconia Catalyst (2006)

The novel supported zirconia catalysts for the synthesis of methyl N-phenyl carbamate (MPC) from aniline and dimethyl carbonate (DMC) are investigated. The unknown byproduct is determined as N,N-dimethylaniline (DMA) by GC−MS. The basic thermodynamics data of the main reaction and side reactions are calculated using Benson's bond addition method. The results show that the synthesis of N-methylaniline (NMA) and DMA are the main competitive reactions to MPC synthesis. It is found that the best support for supported zirconia catalyst is SiO2 and that the best loading amount is 1%. The optimal reaction conditions over ZrO2/SiO2 are as follows: reaction temperature, 443.15 K; reaction time, 7 h; n(DMC)/n(aniline) = 20; catalyst/aniline = 25 wt %; the conversion of aniline is 98.6%; and the yield of MPC is 79.8%. The results of characterization for the fresh catalyst and the deactivated catalyst show that the decrease of the specific surface area is the reason for deactivation.