gebhart/patrepeval huggingface dataset:
Exome Sequencing and Prediction of Long-Term Kidney Allograft Function (2015)

Abstract Current strategies to improve graft outcome following kidney transplantation consider information at the HLA loci. Here, we used exome sequencing of DNA from ABO compatible kidney graft recipients and their living donors to determine recipient and donor mismatches at the amino acid level over entire exomes. We estimated the number of amino acid mismatches in transmembrane proteins, more likely to be seen as foreign by the recipient’s immune system, and designated this tally as the allogenomics mismatch score (AMS). The AMS can be measured prior to transplantation with DNA for potential donor and recipient pairs. We examined the degree of relationship between the AMS and post-transplantation kidney allograft function by linear regression. In a discovery cohort, we found a significant inverse correlation between the AMS and kidney graft function at 36 months post-transplantation (n=10 recipient/donor pairs; 20 exomes) (r 2 >=0.57, P<0.05). The predictive ability of the AMS persists when the score is restricted to regions outside of the HLA loci. This relationship was validated using an independent cohort of 24 recipient donor pairs (n=48 exomes) (r 2 >=0.39, P<0.005). In an additional cohort of living and mostly intra-familial recipient/donor pairs (n=19, 38 exomes), we validated the association after controlling for donor age at time of transplantation. Finally, a model that controls for donor age, HLA mismatches and time post-transplantation yields a consistent AMS effect across these three independent cohorts (P<0.05). Taken together, these results show that the AMS is a strong predictor of long-term graft function in kidney transplant recipients. One Sentence Summary Prediction of long-term kidney graft function with exome sequencing
A two-dimensional decomposition approach for matrix completion through gossip (2017)

Factoring a matrix into two low rank matrices is at the heart of many problems. The problem of matrix completion especially uses it to decompose a sparse matrix into two non sparse, low rank matrices which can then be used to predict unknown entries of the original matrix. We present a scalable and decentralized approach in which instead of learning two factors for the original input matrix, we decompose the original matrix into a grid blocks, each of whose factors can be individually learned just by communicating (gossiping) with neighboring blocks. This eliminates any need for a central server. We show that our algorithm performs well on both synthetic and real datasets.
The Laser‐Controlled Micrometer‐Scale Photoelectrochemical Etching of III–V Semiconductors (1991)

Laser‐controlled photoelectrochemical etching of III–V semiconductors using micrometer‐sized illumination regions has been investigated for varying laser parameters (power, spot size, wavelength) and etching solutions. The etching has been applied to a wide variety of semiconductor doping types. The micrometer spot size of the laser can induce higher etch rates for a given intensity when compared to broad illumination. In addition, the process has micrometer‐scale resolution and highly directional etch anisotropy. In this electroless process the laser etching rate is influenced by light‐induced voltage shifts in the surface potential. Finally, the dependence of the process resolution on carrier diffusion and etch depth is discussed.
Wafer level build-up stacking process using molten metal filling for multi-chip packaging (2012)

TSV (Through-Silicon Via) 3D packaging technology has been and continues to be investigated by many of the semiconductor manufacturer and research institute as a practical way to achieve higher performance and smaller form factors. Compared with conventional 2D packaging, this can increase packing density and reduce power consumption dramatically because of shorter interconnection by vertical directional stacking. So far 3D stacking technology based on W2W bonding has developed widely such as 3D Image sensor and 3D stacking memory because it has the advantage of easier alignment and higher throughput compared with chip-to-chip bonding. However, the wafer level 3D stacking method can be only applicable to products with high production yield because overall yield of 3D stacking chips depends on the yield of multiple stacked layers. In this paper, we suggested wafer level build-up stacking process using oxide bonding and molten metal filling newly, which temporary bonding process is unnecessary and demonstrated it through experiments.
Activation of the Herpes Simplex Virus Type 1 Protease (1995)

The catalytic efficiency of the mature HSV-1 protease has been examined as a function of solvent composition. With the peptide substrate HTYLQASEKFKMWG-amide, the specificity constant (kcat/Km) at pH 7.5 for cleavage is 5.2 M-1 s-1. This value increases to 38 M-1 s-1 when 25% glycerol is present in the reaction mixture. It was found that glycerol activation is but one case of the general phenomenon of HSV-1 protease activation by kosmotropes, or water structure-forming cosolvents. For example, an 860-fold increase in the protease activity (kcat/Km = 4500 M-1 s-1) occurs in the presence of 0.8 M sodium citrate. Similarly, the presence of 0.8 M sodium phosphate activates the catalytic efficiency by 420-fold (kcat/Km = 2200 M-1 s-1). The extent of HSV-1 protease activation by various anions correlates with the Hofmeister series. Both the susceptibility to proteolysis by trypsin and the protein fluorescence spectra of the HSV-1 protease change in the presence of activating solvents, suggesting a conformational change accompanying activation.
D-PuP: An enhanced prediction algorithm for real-time MPEG-4 VBR video traffic with dynamic adaptation (2008)

In previous work [1], we proposed a real-time MPEG-4 VBR video traffic prediction algorithm that calculates the probability density function (PDF) based on the last N frames, rWin, by using Cubic-spline interpolation method, and then utilize it for the prediction of next frame. We fixed the size of rWin as five in the algorithm. Although the algorithm is capable of providing more accurate prediction than those in the research literature, it still has weakness on the adapting the traffic dynamics due to the fixed size of rWin. In this paper, we first study the experimental investigation about the number of rWin, and propose an enhanced traffic prediction algorithm with dynamic rWin.
Diode-pumped optical parametric oscillator (1996)

Diode-pumped optical parametric oscillation has been demonstrated for the first time to our knowledge in a single Nd:MgO:LiNbO(3) nonlinear crystal. The crystal is pumped by a semiconductor diode laser array at 812 nm. The Nd(3+) ions absorb the 812-nm radiation to generate 1084-nm laser oscillation. On internal Q switching the 1084-nm radiation pumps the LiNbO(3) host crystal that is angle cut at 46.5 degrees and generates optical parametric oscillation. The oscillation threshold that is due to the 1084-nm laser pump with a pulse length of 80 ns in a 1-mm-diameter beam was measured to be approximately 1 mJ and produced 0.5-mJ output at 3400-nm signal wavelength.
Arsenic remediation of drinking water using iron-oxide coated coal bottom ash (2010)

We describe laboratory and field results of a novel arsenic removal adsorbent called 'Arsenic Removal Using Bottom Ash' (ARUBA). ARUBA is prepared by coating particles of coal bottom ash, a waste material from coal fired power plants, with iron (hydr)oxide. The coating process is simple and conducted at room temperature and atmospheric pressure. Material costs for ARUBA are estimated to be low (approximately $0.08 per kg) and arsenic remediation with ARUBA has the potential to be affordable to resource-constrained communities. ARUBA is used for removing arsenic via a dispersal-and-removal process, and we envision that ARUBA would be used in community-scale water treatment centers. We show that ARUBA is able to reduce arsenic concentrations in contaminated Bangladesh groundwater to below the Bangladesh standard of 50 ppb. Using the Langmuir isotherm (R(2) = 0.77) ARUBA's adsorption capacity in treating real groundwater is 2.6 x 10(- 6)mol/g (0.20 mg/g). Time-to-90% (defined as the time interval for ARUBA to remove 90% of the total amount of arsenic that is removed at equilibrium) is less than 1 hour. Reaction rates (pseudo-second-order kinetic model, R(2) > or = 0.99) increase from 2.4 x 10(5) to 7.2 x 10(5) g mol(- 1)min(- 1) as the groundwater arsenic concentration decreases from 560 to 170 ppb. We show that ARUBA's arsenic adsorption density (AAD), defined as the milligrams of arsenic removed at equilibrium per gram of ARUBA added, is linearly dependent on the initial arsenic concentration of the groundwater sample, for initial arsenic concentrations of up to 1600 ppb and an ARUBA dose of 4.0 g/L. This makes it easy to determine the amount of ARUBA required to treat a groundwater source when its arsenic concentration is known and less than 1600 ppb. Storing contaminated groundwater for two to three days before treatment is seen to significantly increase ARUBA's AAD. ARUBA can be separated from treated water by coagulation and clarification, which is expected to be less expensive than filtration of micron-scale particles, further contributing to the affordability of a community-scale water treatment center.
Macroporous silicon UV filters for space and terrestrial environments (2004)

Currently used optical filters exhibit strong limitations in the deep UV and shorter wavelength ranges. We propose an entirely different type of UV filter to solve many of the problems due to inadequate materials and fabrication techniques. These filters consist of three-dimensionally ordered Macroporous Silicon (MPSi), with the pores used as waveguide cores separated by the reflective silicon host. Ordered pores serve as a two-dimensional array of optical waveguides. Multilayer coating of the pore walls results in the band-pass, short-pass, or band-blocking transmittance spectra of MPSi filters. Such filters have a number of advantages. They do not exhibit spectral shifts of the passed or blocked spectral bands with the angle of incidence, permitting operation in tilted and divergent light beams to simplify optical system design and fabrication. Due to their structures (fewer and thinner layers on the pore walls required to gain the same level of rejection), the filters do not exhibit delamination problems and are well suited for operation at extreme temperatures (for space as well as for terrestrial environments). The fabrication process is different from that used for multilayer interference filters. This process permits the fabrication of filters up to 200mm in diameter that are suitable for wavelengths from longer than 400 nm to shorter than 100 nm. Far-UV filters can be manufactured as simply and economically as the near UV ones. The theory of light propagation through the MPSi layers is developed, the main predictions of the theory are experimentally validated, and the fabrication procedure for MPSi UV filters is reported.
A time-dependent clustering model for non-uniform dielectric breakdown (2013)

We report a time-dependent clustering model for non-uniform dielectric breakdown. While at high percentiles non-Possion area scaling dominates, the model restores the weakest-link characteristics at low percentiles relevant for reliability projection. Its validity is demonstrated by area scaling and excellent agreement with multiple experimental data sets. We show the clustering model can replace Weibull model with largely improved reliability margins.
Expansion of Dysfunctional Tim-3–Expressing Effector Memory CD8+ T Cells during Simian Immunodeficiency Virus Infection in Rhesus Macaques (2014)

The T cell Ig- and mucin domain-containing molecule-3 (Tim-3) negative immune checkpoint receptor demarcates functionally exhausted CD8(+) T cells arising from chronic stimulation in viral infections like HIV. Tim-3 blockade leads to improved antiviral CD8(+) T cell responses in vitro and, therefore, represents a novel intervention strategy to restore T cell function in vivo and protect from disease progression. However, the Tim-3 pathway in the physiologically relevant rhesus macaque SIV model of AIDS remains uncharacterized. We report that Tim-3(+)CD8(+) T cell frequencies are significantly increased in lymph nodes, but not in peripheral blood, in SIV-infected animals. Tim-3(+)PD-1(+)CD8(+) T cells are similarly increased during SIV infection and positively correlate with SIV plasma viremia. Tim-3 expression was found primarily on effector memory CD8(+) T cells in all tissues examined. Tim-3(+)CD8(+) T cells have lower Ki-67 content and minimal cytokine responses to SIV compared with Tim-3(-)CD8(+) T cells. During acute-phase SIV replication, Tim-3 expression peaked on SIV-specific CD8(+) T cells by 2 wk postinfection and then rapidly diminished, irrespective of mutational escape of cognate Ag, suggesting non-TCR-driven mechanisms for Tim-3 expression. Thus, rhesus Tim-3 in SIV infection partially mimics human Tim-3 in HIV infection and may serve as a novel model for targeted studies focused on rejuvenating HIV-specific CD8(+) T cell responses.
Dickkopf 1 (DKK1) regulates skin pigmentation and thickness by affecting Wnt/ β‐catenin signaling in keratinocytes (2007)

The epidermis (containing primarily keratinocytes and melanocytes) overlies the dermis (containing primarily fibroblasts) of human skin. We previously reported that dickkopf 1 (DKK1) secreted by fibroblasts in the dermis elicits the hypopigmented phenotype of palmoplantar skin due to suppression of melanocyte function and growth via the regulation of two important signaling factors, microphthalmia-associated transcription factor (MITF) and beta-catenin. We now report that treatment of keratinocytes with DKK1 increases their proliferation and decreases their uptake of melanin and that treatment of reconstructed skin with DKK1 induces a thicker and less pigmented epidermis. DNA microarray analysis revealed many genes regulated by DKK1, and several with critical expression patterns were validated by reverse transcriptase-polymerase chain reaction and Western blotting. DKK1 induced the expression of keratin 9 and alpha-Kelch-like ECT2 interacting protein (alphaKLEIP) but down-regulated the expression of beta-catenin, glycogen synthase kinase 3beta, protein kinase C, and proteinase-activated receptor-2 (PAR-2), which is consistent with the expression patterns of those proteins in human palmoplantar skin. Treatment of reconstructed skin with DKK1 reproduced the expression patterns of those key proteins observed in palmoplantar skin. These findings further elucidate why human skin is thicker and paler on the palms and soles than on the trunk through topographical and site-specific differences in the secretion of DKK1 by dermal fibroblasts that affects the overlying epidermis.
The Desired Memristor for Circuit Designers (2013)

Memristors are two-terminal devices with varying resistance, where the behavior is dependent on the history of the device. In recent years, different physical phenomena of resistive switching have been linked with the theoretical concept of a memristor, and several emerging memory devices (e.g., Phase Change Memory, Resistive RAM, STT-MRAM) are now considered as memristors. Memristors hold promise for use in diverse applications such as memory, digital logic, analog circuits, and neuromorphic systems. Important characteristics of memristors include high speed, low power, good scalability, data retention, endurance, and compatibility with conventional CMOS in terms of manufacturing and operating voltages. One interesting property of some memristors is a nonlinear response to current or voltage. Nonlinear memristors exhibit a current or voltage threshold, such that the resistance is affected only by currents or voltages which exceed the threshold, while the resistance of a linear memristor changes with small perturbations in device current. Different applications exploit different characteristics of a memristor. In this article, the desired characteristics for different applications are presented from the viewpoint of an integrated circuit designer. Understanding the desired characteristics for different applications can assist device and material engineers in providing the appropriate behavior when developing memristive devices, thereby optimizing these devices for different applications.
Two-dimensional photonic bandgap defect laser (2003)

We have demonstrated optically pumped two-dimensional photonic crystal defect InGaAsP MQW lasers at 1.5 /spl mu/m. Pulsed lasing action at 143 K has been obtained in microcavities as small as 2(/spl lambda//2n)/sup 3/.
Overexpression of nerve growth factor in transgenic mice induces novel sympathetic projections to primary sensory neurons (1994)

Peripheral nerve crush induces novel projections from noradrenergic sympathetic neurons to sensory ganglia, and it has been suggested that these projections provide an anatomical substrate for chronic pain syndromes that occur after nerve injury. The present study demonstrates that novel sympathetic projections to sensory neurons are also induced in transgenic mice that overexpress nerve growth factor (NGF) in the skin. Specifically, a large proportion of trigeminal neurons in NGF transgenic mice were innervated by tyrosine hydroxylase (TH)-positive pericellular arborizations that were seen only rarely in controls. Electron microscopic analysis of NGF transgenic mice revealed that trigeminal neurons were surrounded by numerous axonal varicosities containing synaptic specializations. Removal of the superior cervical ganglion abolished TH-immunoreactive arborizations in the ipsilateral trigeminal ganglion confirming that these fibers were sympathetic axons. A two-site enzyme-linked immunosorbent assay revealed that transgenic ganglia contained a tenfold increase in NGF peptide compared to controls. However, reverse transcriptase polymerase chain reaction analysis showed no apparent expression of transgene mRNA in sensory ganglia, suggesting that the additional NGF was derived from increased NGF expression in the skin. These results indicate that NGF can induce novel sympathetic projections to sensory neurons in vivo and suggests a model in which increased NGF expression plays a role in the development of sympathetic hyperalgesia after nerve injury.
VideoGraph: Recognizing Minutes-Long Human Activities in Videos (2019)

Many human activities take minutes to unfold. To represent them, related works opt for statistical pooling, which neglects the temporal structure. Others opt for convolutional methods, as CNN and Non-Local. While successful in learning temporal concepts, they are short of modeling minutes-long temporal dependencies. We propose VideoGraph, a method to achieve the best of two worlds: represent minutes-long human activities and learn their underlying temporal structure. VideoGraph learns a graph-based representation for human activities. The graph, its nodes and edges are learned entirely from video datasets, making VideoGraph applicable to problems without node-level annotation. The result is improvements over related works on benchmarks: Epic-Kitchen and Breakfast. Besides, we demonstrate that VideoGraph is able to learn the temporal structure of human activities in minutes-long videos.
Enzymatic synthesis of nucleoside antibiotics. Part II. Microbial synthesis of purine arabinosides and their biological activity. (1985)

A simple method for the synthesis of various purine arabinosides from purine bases and uracil arabinoside by microbial transarabinosylation is described. A wet cell paste of Enterobacter aerogenes AJ 11125 showed a wide substrate specificity range for purine bases. Not only naturally occurring purine bases such as adenine and hypoxanthine but also unnatural bases such as 6-thioguanine and 2-chlorohypoxanthine were catalyzed to give the corresponding purine arabinosides. The enzymatically synthesized purine arabinosides were isolated from the reaction mixtures and identified by physicochemical means. The biological activities of the compounds were investigated and it was found that thioguanine arabinoside and 2-methyladenine arabinoside have potent activity against Hela cells, and their ED50 were 10.5 and 21.5μg/ml, respectively.
Kinetic Selectivity of Olefin Metathesis Catalysts Bearing Cyclic (Alkyl)(Amino)Carbenes (2008)

The evaluation of ruthenium olefin metathesis catalysts 4-6 bearing cyclic (alkyl)(amino)carbenes (CAACs) in the cross-metathesis of cis-1,4-diacetoxy-2-butene (7) with allylbenzene (8) and the ethenolysis of methyl oleate (11) is reported. Relative to most NHC-substituted complexes, CAAC-substituted catalysts exhibit lower E/Z ratios (3:1 at 70% conversion) in the cross-metathesis of 7 and 8. Additionally, complexes 4-6 demonstrate good selectivity for the formation of terminal olefins versus internal olefins in the ethenolysis of 11. Indeed, complex 6 achieved 35 000 TONs, the highest recorded to date. CAAC-substituted complexes exhibit markedly different kinetic selectivity than most NHC-substituted complexes.
Simultaneous measurement of multichannel laser linewidths using stimulated Brillouin scattering (2002)

In this paper, we introduce a novel measurement technique using stimulated Brillouin scattering (SBS) in the fiber. Here, instead of the frequency shifted by an acousto-optic modulator in the self delayed heterodyne beating (SDHB), the shifted frequency from the SBS is used to downscale the channel spacing. As a result, it is possible to simultaneously measure multichannel linewidths in the same window of an spectrum analyzer.
Engineering of xylose reductase and overexpression of xylitol dehydrogenase and xylulokinase improves xylose alcoholic fermentation in the thermotolerant yeast Hansenula polymorpha (2008)

Recombinant strains of H. polymorpha engineered for improved xylose utilization are described in the present work. These strains show a significant increase in ethanol productivity with simultaneous reduction in the production of xylitol during high-temperature xylose fermentation.
“Unleaded” Perovskites: Status Quo and Future Prospects of Tin‐Based Perovskite Solar Cells (2018)

The tremendous interest focused on organic-inorganic halide perovskites since 2012 derives from their unique optical and electrical properties, which make them excellent photovoltaic materials. Pb-based halide perovskite solar cells, in particular, currently stand at a record efficiency of ≈23%, fulfilling their potential toward commercialization. However, because of the toxicity concerns of Pb-based perovskite solar cells, their market prospects are hindered. In principle, Pb can be replaced with other less-toxic, environmentally benign metals. Sn-based perovskites are thus the far most promising alternative due to their very similar and perhaps even superior semiconductor characteristics. After years of effort invested in Sn-based halide perovskites, sufficient breakthroughs have finally been achieved that make them the next runners up to the Pb halide perovskites. To help the reader better understand the nature of Sn-based halide perovskites, their optical and electrical properties are systematically discussed. Recent progress in Sn-based perovskite solar cells, focusing mainly on film fabrication methods and different device architectures, and highlighting roadblocks to progress and opportunities for future work are reviewed. Finally, a brief overview of mixed Sn/Pb-based systems with their anomalous yet beneficial optical trends are discussed. The current challenges and a future outlook for Sn-based perovskites are discussed.