gebhart/patrepeval huggingface dataset:
Derivation of an amino acid similarity matrix for peptide:MHC binding and its application as a Bayesian prior (2009)

A novel amino acid similarity matrix has been derived for peptide:MHC binding interactions. One prominent feature of the matrix is that it disfavors substitution of residues with opposite charges. Given that the matrix was derived from experimentally determined peptide:MHC binding affinity measurements, this feature is likely shared by all peptide:protein interactions. In addition, we have demonstrated the usefulness of the matrix as a Bayesian prior in an improved scoring-matrix based peptide:MHC class I prediction method. A software implementation of the method is available at: http://www.mhc-pathway.net/smmpmbec.
Generation of a chimeric human and simian immunodeficiency virus infectious to monkey peripheral blood mononuclear cells (1991)

We constructed five chimeric clones between human immunodeficiency virus type 1 (HIV-1) and simian immunodeficiency virus (SIVMAC) and four SIVMAC mutants by recombinant DNA techniques. Three chimeric clones and all mutants with an alteration in either the vif, vpx, vpr, or nef gene were infectious to human CD4-positive cell lines. The susceptibility of macaque monkey peripheral blood mononuclear cells (PBMC) to infection by these mutants and chimeras was examined in vitro. Macaque PBMC supported the replication of wild-type and vpx, vpr, and nef mutant SIVMAC strains. A chimera carrying the long terminal repeats (LTRs), gag, pol, vif, and vpx of SIVMAC and tat, rev, vpu, and env of HIV-1 was also replication competent in PBMC. In contrast, HIV-1, the vif mutant of SIVMAC, a chimera containing rev and env of SIVMAC, and a chimera containing vpx, vpr, tat, rev, and env of SIVMAC did not grow in PBMC. Western immunoblotting analysis of the replicating chimera in PBMC confirmed the hybrid nature of the virus. These data strongly suggested that the sequence important for macaque cell tropism lies within the LTR, gag, pol, and/or vif sequences of the SIVMAC genome.
Vitamin E Intake and Risk of Cataracts in Humansa (1989)

Experimental evidence suggests that oxidative stress due to the accumulation of free radicals plays a role in the pathogenesis of cataracts and that the process can be prevented or ameliorated by antioxidants. In addition, a recent study found that cataract patients tended to have lower serum levels of vitamins C, E, or carotenoids than did control subjects. This investigation, which compared the self-reported consumption of supplementary vitamins by 175 cataract patients with that of 175 individually matched, cataract-free subjects, revealed that the latter group used significantly more supplementary vitamins C and E (p = 0.01 and 0.004, respectively). Inasmuch as the observed reduction in risk of cataracts was at least 50%, a randomized, controlled trial of vitamin supplementation in cataract prevention seems justified.
Structural characterization of low molecular weight heparins. (1999)

Low molecular weight heparins (LMWHs) obtained by different depolymerization processes can be distinguished from each other by characteristic end-residues, which are easily identified and quantified by nuclear-magnetic-resonance (NMR) spectroscopy. NMR spectroscopy characterizes major sulfation patterns as well as minor sequences such as the antithrombin-binding sequence and the linkage region of LMWHs. Artifacts associated with base-induced modifications such as the formation of iduronic acid epoxide and aziridine derivatives of N-sulfoglucosamine residues can also be detected. The influence of these modifications on the binding of heparins and LMWHs to proteins other than antithrombin are discussed.
Quinolone‐ResistantSalmonella typhiin Viet Nam: Molecular Basis of Resistance and Clinical Response to Treatment (1997)

Nalidixic acid-resistant Salmonella typhi (NARST) was first isolated in Viet Nam in 1993. Analysis of the quinolone resistance-determining region of gyrA in 20 NARST isolates by polymerase chain reaction and single-stranded conformational polymorphism yielded two novel patterns: pattern II corresponding to a point mutation at nucleotide 87 Asp-->Gly (n = 17), and pattern III corresponding to a point mutation at nucleotide 83 Ser-->Phe (n = 3). In trials of short-course ofloxacin therapy for uncomplicated typhoid, 117 (78%) of 150 patients were infected with multidrug-resistant S. typhi, 18 (15%) of which were NARST. The median time to fever clearance was 156 hours (range, 30-366 hours) for patients infected with NARST and 84 hours (range, 12-378 hours) for those infected with nalidixic acid-susceptible strains (P < .001). Six (33.3%) of 18 NARST infections required retreatment, whereas 1 (0.8%) of 132 infections due to susceptible strains required retreatment (relative risk = 44; 95% confidence interval = 5.6-345; P < .0001). We recommend that short courses of quinolones not be used in patients infected with NARST.
Multimode Small-Signal Analysis of Side-Mode Injection-Locked Semiconductor Lasers (1992)

Temporal response of side-mode injection-locked semiconductor lasers is studied using a small signal analysis of multimode rate equations. The relaxation oscillation frequency and the decay rate are shown to be sensitive to the choice of the injection target mode. Modes with shorter wavelengths have higher relaxation frequencies due to their larger differential gain. Maximum enhancement of the relaxation frequency occurs within that group of target modes. The analysis, together with the previously predicted enhancement of stable locking range, suggests feasibility of applying the side-mode injection technique to increase the modulation bandwidth of semiconductor lasers and hence the transmission speed in optical communication systems, while preserving the usual benefits of injection locking.
Ovaries Remain Functional in Squirrel Monkeys (Saimiri sciureus) Immunized with Porcine Zona Pellucida 55,000 Macromolecule1 (1987)

Fifty female squirrel monkeys were each immunized with 200 micrograms of a purified preparation of the 55,000 macromolecule (ZP3) from porcine zona pellucida. The fertility status of these immunized monkeys, as well as the effect of ZP3 antibodies on ovarian function, was monitored. High anti-ZP3 titers were achieved (greater than 75% binding levels as determined by radioimmunoassay) and remained high (approximately 67% binding level) for the duration of this study. Hormonal evaluations indicated initial disturbances in normal ovarian steroid secretion and function that were confirmed by laparoscopic observation and oocyte production data. Histological examination of ovaries at 6-7 mo post-injection suggested an interference in folliculogenesis. No pregnancies were observed in the immunized monkeys during this period. By 10-15 mo post-immunization, hormonal and laparoscopic data indicated that ovarian function was recovering in injected monkeys despite the continued presence of high titers to ZP3. Collectively, these results demonstrate that although immunization with ZP3 initially produces disturbances in normal ovarian function that inhibit fertility, these effects are reversible. Such findings encourage the continued intensive investigation of purified porcine zona macromolecules for immunocontraceptive purposes.
Open quantum spin systems in semiconductor quantum dots and atoms in optical lattices (2012)

In this thesis, we study open quantum spin systems from several perspectives. We propose the realization of a quantum interface between a traveling-wave light field and the nuclear spins in a quantum dot coupled to a cavity. Our scheme is robust against cavity decay and allows for high-fidelity write-in and read-out. We present a theoretical description of an experiment in which highly asymmetric dynamic nuclear spin pumping is observed in a self-assembled quantum dot. Moreover, we propose a scheme to realize a quantum spin system using ultracold atoms in an optical lattice in which both coherent interaction and dissipation can be engineered. We find that the steady state expectation values of different spin models exhibit discontinuous behaviour at degeneracy points of the Hamiltonian for weak dissipation. We moreover study spin models under the aspect of state preparation and spin chains with subwavelength interatomic distances.
Energy-aware adaptation for mobile applications (1999)

In this paper, we demonstrate that a collaborative relationship between the operating system and applications can be used to meet user-specified goals for battery duration. We first show how applications can dynamically modify their behavior to conserve energy. We then show how the Linux operating system can guide such adaptation to yield a battery-life of desired duration. By monitoring energy supply and demand, it is able to select the correct tradeoff between energy conservation and application quality. Our evaluation shows that this approach can meet goals that extend battery life by as much as 30%.
Chemical Detection with a Single-Walled Carbon Nanotube Capacitor (2005)

We show that the capacitance of single-walled carbon nanotubes (SWNTs) is highly sensitive to a broad class of chemical vapors and that this transduction mechanism can form the basis for a fast, low-power sorption-based chemical sensor. In the presence of a dilute chemical vapor, molecular adsorbates are polarized by the fringing electric fields radiating from the surface of a SWNT electrode, which causes an increase in its capacitance. We use this effect to construct a high-performance chemical sensor by thinly coating the SWNTs with chemoselective materials that provide a large, class-specific gain to the capacitance response. Such SWNT chemicapacitors are fast, highly sensitive, and completely reversible.
The Quaternary Pan-lake （Overflow） Period and Paleoclimate on the Qinghai-Tibet Plateau (2005)

Lake geomorphology and high-level lacustrine deposits since the mid-late Pleistocene are well preserved in lakes of the Qinghai-Tibet Plateau. According to geological surveys of 17 lake districts in different locations of the plateau,combined with interpretations of satellite images and topographic maps, the authors studied the timing of formation and scopes of the pan-lake areas of the plateau and their paleoclimate. The latest two high lake levels (overflow surfaces) on the Qinghai-Tibet Plateau in the Quaternary occurred at ～40 to 30/35 ka and ～65 to 53 ka respectively. In these time intervals, the plateau was covered by huge interconnected pan-lake systems with a total area of ～36 km2 and a total volume of lake water of ＞530 million km2, which are about 38 times and 659 times larger than those of the modem lakes respectively. Before this pan-lake period in the late Pleistocene, there had been three high lake levels that occurred at ～132-112 ka, 110-95 ka and 91-72/～83-75 ka respectively, suggesting that the late Quaternary climate on the plateau was unstable and changed rapidly. The ～40-30 ka high lake level also appeared in the Tengger desert north of the plateau,suggesting that there existed very strong summer monsoons from South Asia then; the variation in solar radiation with a 20,000 precessional period has special importance for the high-altitude Qinghai-Tibet Plateau in the low-latitude zone of the Earth. Around 30 ka, the pan-lakes at the peripheries of the Qinghai-Tibet Plateau drained out suddenly with rapid uplift of the plateau and cooling. In a short time the huge amount of cold lake water emptied into the Indian Ocean and Western Pacific. The draining event of the pan-lakes brought about the environmental changes of rivers and lakes at peripheries of the plateau.
WNT5A-mediated -catenin-independent signalling is a novel regulator of cancer cell metabolism (2013)

WNT5A has been identified as an important ligand in the malignant progression of a number of tumours. Although WNT5A signalling is often altered in cancer, the ligand's role as either a tumour suppressor or oncogene varies between tumour types and is a contemporary issue for investigators of β-catenin-independent WNT signalling in oncology. Here, we report that one of the initial effects of active WNT5A signalling in malignant melanoma cells is an alteration in cellular energy metabolism and specifically an increase in aerobic glycolysis. This was found to be at least in part due to an increase in active Akt signalling and lactate dehydrogenase (LDH) activity. The clinical relevance of these findings was strengthened by a strong correlation (P < 0.001) between the expression of WNT5A and LDH isoform V in a cohort of melanocytic neoplasms. We also found effects of WNT5A on energy metabolism in breast cancer cells, but rather than promoting aerobic glycolysis as it does in melanoma, WNT5A signalling increased oxidative phosphorylation rates in breast cancer cells. These findings support a new role for WNT5A in the metabolic reprogramming of cancer cells that is a context- dependent event.
Chimeric muscarinic cholinergic: beta-adrenergic receptors that activate Gs in response to muscarinic agonists. (1990)

The M1-muscarinic cholinergic receptor (M1AChR) stimulates the release of inositol phosphates (IPs) but does not activate adenylyl cyclase. The beta-adrenergic receptor (beta-AR) stimulates adenylyl cyclase but has no effect on IP release. Amino acid sequences corresponding to the second (I2) and third (I3) intracellular loops of the turkey erythrocyte beta-AR and a 12-amino acid segment near the N-terminal end of the I3 region were substituted into the corresponding regions of the human M1AChR. Chimeric receptors that contained either the entire I3 loop or the N-terminal dodecapeptide of that loop both mediated the 2-4-fold stimulation of adenylyl cyclase activity in membrane fractions of COS, A293, or Sf9 cells in response to carbachol. These chimeric receptors also retained the ability to stimulate IP release to the same extent as did the M1AChR. In COS cells transfected with the I3 chimeric receptor, the EC50 for carbachol was approximately 7 microM for the stimulation of adenylyl cyclase and approximately 2 microM for the release of IP; M1AChR-mediated IP release displayed an EC50 of approximately 0.2 microM. Substitution of the I2 region of the beta-AR into the M1AChR did not by itself alter selectivity for signaling. However, the I2+I3 and I2+dodecapeptide combined replacements stimulated adenylyl cyclase fully and caused at most 25% of the maximal stimulation of IP release observed with the M1AChR. Thus, a small region in the third cytoplasmic loop can alter the G proteins to which a receptor is coupled, but interaction among loops is evidently involved in fully determining G protein selectivity.
Not only lithium: regulation of glycogen synthase kinase-3 by antipsychotics and serotonergic drugs (2006)

Multiple recent lines of evidence have underscored the potential role of glycogen synthase kinase-3 (GSK3) as a common molecular signal integrator and therapeutic target for different classes of psychiatric drugs (Figure 1). GSK3α and GSK3β are two closely related serine/threonine kinases originally associated with the regulation of glycogen synthesis in response to insulin (Embi et al., 1980). These constitutively active kinases are regulated negatively through the phosphorylation of single serine residues, Ser21 (GSK3α) and Ser9 (GSK3β), of their regulatory amino-terminal domain (Frame and Cohen, 2001). The protein kinase Akt/PKB has been shown to inhibit both GSK3 isoforms in response to insulin and insulin growth factors (Cross et al., 1995). However, other protein kinases such as PKA and PKC can also regulate GSK3 in different cellular systems (Frame and Cohen, 2001). Apart from its function in glycogenesis, GSK3 plays a role in a host of physiological processes including neurodevelopment, cell proliferation and apoptosis. Moreover, dysregulation of GSK3 function is involved in tumour proliferation as well as in the formation of neurofibrillary tangles in Alzheimer's disease (Woodgett, 2003).
IMPROVEMENTS ON SOURCE CAMERA-MODEL IDENTIFICATION BASED ON CFA INTERPOLATION (2005)

The idea of using traces of interpolation algorithms, deployed by a digital camera, as an identifier in the source camera-model identification problem has been initially studied in [2]. In this work, we improve our previous approach by incorporating methods to better detect the interpolation artifacts in smooth image parts. To identify the source cameramodel of a digital image, new features that can detect traces of low-order interpolation are introduced and used in conjunction with a support vector machine based multi-class classifier. Performance results due to newly added features are obtained considering source identification among two and three digital cameras. Also, these results are combined with those of [2] to further improve our methodology.
p-Nitrophenyl and cholesteryl-N-alkyl carbamates as inhibitors of cholesterol esterase. (1987)

p-Nitrophenyl and cholesteryl-N-alkyl carbamates are good inhibitors of porcine pancreatic cholesterol esterase-catalyzed hydrolysis of p-nitrophenyl butyrate. p-Nitrophenyl-N-butyl and N-octyl carbamates (compounds 1 and 2, respectively) are potent active site-directed irreversible inhibitors of this enzyme. The inhibition of cholesterol esterase by compound 1 or 2 shows saturation kinetics with increasing inhibitor concentration. The activity of cholesterol esterase in the presence of compound 1 or 2 can be protected by the competitive inhibitor, phenylboronic acid. First-order decreases in cholesterol esterase activity effected by compound 1 or 2 are also observed in the presence of taurocholate/phosphatidylcholine micelles. Dilution of the inhibited enzyme results in a gradual return of activity, the rate of which is increased in the presence of the nucleophile hydroxylamine. Hence, inhibition of cholesterol esterase-catalyzed hydrolysis of p-nitrophenyl butyrate by compound 1 or 2 in the aqueous or micellar phase occurs via a carbamyl-cholesterol esterase mechanism. The turnover of the butyl carbamylenzyme is increased in the presence of micelles, which indicates that the micelles have a direct effect on the catalytic activity of the enzyme. However, this effect is dependent on the structure of the substrate as the turnover of the octyl carbamylenzyme is unaffected in the presence of micelles. A comparison of the second-order rate constants for the inhibition of cholesterol esterase by compound 1 or 2 indicates that the octyl derivative is the more potent inhibitor. Cholesteryl-N-alkyl carbamates do not carbamylate cholesterol esterase but instead act as reversible inhibitors. This is due to the stability of cholesteryl carbamates relative to p-nitrophenyl carbamates.
Isotretinoin and Cutaneous Helper T-Cell Lymphoma (Mycosis Fungoides) (1987)

Retinoids, including isotretinoin, have demonstrated antiproliferative and antineoplastic activity in laboratory and clinical trials. In a phase II trial, 25 patients with extensive mycosis fungoides were evaluated for response to isotretinoin. There was a 44% (11 patients) objective clinical response rate with three clinical complete responses without concomitant evidence of pathologic clearing of the disease. An additional 24% (six patients) showed a minor degree of clinical improvement. The median time to response was two months (range, 0.5 to eight months) and the median response duration was eight months or longer (range, one to 25 months). Chronic toxic reactions consisted primarily of drying of the skin and mucous membranes and resulted in dose reduction in the majority of patients. It is concluded that isotretinoin produces significant clinical benefit to some patients with mycosis fungoides.
Thermogravimetric Measurement of Hydrogen Absorption in Alkali-Modified Carbon Materials (2000)

We have prepared Li-doped multiwall carbon nanotubes and Li- and K-intercalated graphite and measured their hydrogen storage properties using a thermogravimetric analyzer (TGA). In a flowing H2 atmosphere Li-doped nanotubes and Li-intercalated graphite both exhibit a cyclable weight gain between 200 and 400 °C and weight loss between 400 and 500 °C characterized by a distinct and unusual temperature profile. We find, however, that neither H2 nor carbon is required to generate this TGA feature; we observe it even in Li-containing samples measured in flowing Ar without H2 and in LiOH samples measured in either H2 or Ar. Potassium-intercalated graphite shows mass cycling with a different thermal character between 40 and 250 °C, but as with Li, observation of a large cyclable feature does not rely on the presence of H2. In both cases we identify the cycling mass to be absorption/desorption of H2O present as an impurity in the TGA atmosphere. The temperature signatures we observe are strikingly similar to those reported in a recent study of Li- and K-doped carbon nanofibers in which mass uptakes as large as 20 wt % were attributed to hydrogen absorption. When the impurities in the TGA atmosphere are reduced as much as possible we do detect modest weight changes in K-intercalated graphite which we interpret as true hydrogen absorption at 1.3 wt %, of which 0.2 wt % is cyclable. This level of hydrogen absorption is consistent with pressure−composition isotherm measurements on the same material using a gas reaction controller (1.0 wt % total absorption with 0.3 wt % cyclable). We do not detect any evidence of hydrogen absorption by Li-containing carbon materials under our experimental conditions.
Deep Brain Stimulation for Treatment-Resistant Depression (2008)

Treatment-resistant depression is a severely disabling disorder with no proven treatment options once multiple medications, psychotherapy, and electroconvulsive therapy have failed. Based on our preliminary observation that the subgenual cingulate region (Brodmann area 25) is metabolically overactive in treatment-resistant depression, we studied whether the application of chronic deep brain stimulation to modulate BA25 could reduce this elevated activity and produce clinical benefit in six patients with refractory depression. Chronic stimulation of white matter tracts adjacent to the subgenual cingulate gyrus was associated with a striking and sustained remission of depression in four of six patients. Antidepressant effects were associated with a marked reduction in local cerebral blood flow as well as changes in downstream limbic and cortical sites, measured using positron emission tomography. These results suggest that disrupting focal pathological activity in limbic-cortical circuits using electrical stimulation of the subgenual cingulate white matter can effectively reverse symptoms in otherwise treatment-resistant depression. (Reprinted with permission by Neuron, 2005; (45):651–660)
Deep learning for chest radiograph diagnosis: A retrospective comparison of the CheXNeXt algorithm to practicing radiologists (2018)

In this study, we developed and validated a deep learning algorithm that classified clinically important abnormalities in chest radiographs at a performance level comparable to practicing radiologists. Once tested prospectively in clinical settings, the algorithm could have the potential to expand patient access to chest radiograph diagnostics.