gebhart/patrepeval huggingface dataset:
Characterization of low-resistance ohmic contacts to <i>n</i>- and <i>p</i>-type InGaAs (2013)

Multilayer ohmic contacts with differing first metal layers (M = Mo, Pd, Pt) beneath a Ti/Pt diffusion barrier and Au cap were fabricated on n+ and p+-InGaAs, and the relationship between their specific contact resistance and interfacial chemistry was examined. Palladium-based contacts offered the lowest specific contact resistances of ρc=3.2×10−8 and 1.9×10−8 Ω-cm2 to n+- and p+-InGaAs, respectively. The low resistances of the Pd-based contact were correlated with the formation of a uniform PdxInGaAs phase in direct contact with InGaAs, as observed using transmission electron microscopy and energy dispersive spectroscopy. On the other hand, the Mo-based contact to n+ and p+-InGaAs had much higher specific contact resistances, even though its specific contact resistance on lightly doped n-InGaAs was nearly the same as that of the Pd-based contact. The cause of this discrepancy was identified to be the native oxide layer that remained between the contact and semiconductor in the Mo-based contacts, as revealed using transmission electron microscopy, energy dispersive spectroscopy, and electron energy loss spectroscopy. The effect of the native oxide in series with the Schottky barrier is significant only when the contact is doped heavily enough that tunneling of carriers through the Schottky barrier introduces a very low resistance.
Liposidomycins − Synthetic Studies Towards the Ribosyldiazepanone Moiety (2001)

A synthesis of the enantiopure 2-ribosyl-1,4-diazepan-3-one core of liposidomycins, a class of complex lipid nucleoside antibiotics, according to a flexible asymmetric synthesis strategy is described. It involves two building blocks, an enantiopure α-azido-β,γ-epoxybutanol readily available from L-ascorbic acid, and an α-ribosylamino acid obtained from D-ribose. Subsequent cyclization by regiospecific nucleophilic opening of the epoxide by the amino acid followed by peptidic coupling affords the target ribosyl diazepanone.
Funding Research: An Exploration of Inter‐Discipline Variations (1993)

Abstract In 1993, the Higher Education Funding Council for England (HEFCE) introduced a new system for determining the research component of block grant funding to English universities. The inter‐disciplinary differences in the amounts allocated suggest funding anomalies which are not related to the costs of research infrastructure in those disciplines. Analyses of the allocation procedure indicate how those anomalies have come about. I am grateful to the staff of the HEFCE for providing tabulations of unpublished data, and for background information of the allocation procedure, and to Mr R. E. Goodchild for useful discussions and advice.
Using Quantitative BRET to Assess G Protein-Coupled Receptor Homo- and Heterodimerization (2011)

Over a period of 15 years the concept of G protein-coupled receptor (GPCR) dimerization moved from a challenging hypothesis to a scientific fact, which is now accepted by the vast majority of the scientists working in the field. However, several important issues remain debated such as the biological function of dimerization, or the actual complexity of the oligomeric organization. Because of its major potential implications in physiology and pharmacology, the question of GPCR heterodimerization (or hetero-oligomerization) is currently one of the most central. Several complementary experimental approaches are used to investigate these novel important aspects of GPCR biology. In this context, Bioluminescence Resonance Energy Transfer-based techniques are extremely powerful, provided that they are conducted with the appropriate (numerous) controls and correctly interpreted.
The p7 protein of hepatitis C virus forms an ion channel that is blocked by the antiviral drug, Amantadine (2002)

Hepatitis C virus (HCV) cannot be grown in vitro, making biochemical identification of new drug targets especially important. HCV p7 is a small hydrophobic protein of unknown function, yet necessary for particle infectivity in related viruses [Harada, T. et al., (2000) J. Virol. 74, 9498-9506]. We show that p7 can be cross-linked in vivo as hexamers. Escherichia coli expressed p7 fusion proteins also form hexamers in vitro. These and HIS-tagged p7 function as calcium ion channels in black lipid membranes. This activity is abrogated by Amantadine, a compound that inhibits ion channels of influenza [Hay, A.J. et al. (1985) EMBO J. 4, 3021-3024; Duff, K.C. and Ashley, R.H. (1992) Virology 190, 485-489] and has recently been shown to be active in combination with current HCV therapies.
Combinators for bi-directional tree transformations (2005)

We propose a novel approach to the well-known view update problem for the case of tree-structured data: a domain-specific programming language in which all expressions denote bi-directional transformations on trees. In one direction, these transformations---dubbed lenses---map a "concrete" tree into a simplified "abstract view"; in the other, they map a modified abstract view, together with the original concrete tree, to a correspondingly modified concrete tree. Our design emphasizes both robustness and ease of use, guaranteeing strong well-behavedness and totality properties for well-typed lenses.We identify a natural space of well-behaved bi-directional transformations over arbitrary structures, study definedness and continuity in this setting, and state a precise connection with the classical theory of "update translation under a constant complement" from databases. We then instantiate this semantic framework in the form of a collection of lens combinators that can be assembled to describe transformations on trees. These combinators include familiar constructs from functional programming (composition, mapping, projection, conditionals, recursion) together with some novel primitives for manipulating trees (splitting, pruning, copying, merging, etc.). We illustrate the expressiveness of these combinators by developing a number of bi-directional list-processing transformations as derived forms.
SIxD: A Configurable Application-Specific SISD/SIMD Microprocessor Soft-Core (2006)

In this study, an FPGA-based, configurable, application-specific, SIMD-capable, non-pipelined RISC soft processor core that operates on variable-width fixed-point data is presented. The flexible SISD core with general-purpose instructions fits on small FPGAs, but can be easily configured to incorporate application-specific instructions and to operate in SIMD mode when higher performance is required
Interaction of μ‐opioid receptor agonists and antagonists with the analgesic effect of buprenorphine in mice (2005)

Buprenorphine is a potent opioid analgesic with partial agonistic properties at mu-opioid receptors. This study investigated the interaction potential with several full mu-agonists in the tail-flick test in mice. We further examined the reversibility of buprenorphine antinociception by different mu-opioid receptor antagonists. Combination of buprenorphine with morphine, oxycodone, hydromorphone and fentanyl in the analgesic dose range resulted in additive or synergistic effects. When given after the decline of the acute buprenorphine effect, both morphine and fentanyl also showed full efficacy. A moderate antagonistic effect according to the partial mu-agonistic properties of buprenorphine was only seen when high doses exceeding the therapeutic dose ranges were combined. Under these conditions antinociception of morphine was reduced to the effect of buprenorphine alone. Prophylactic administration of naloxone (10 mg/kg i.v.), naltrexone (1 mg/kg i.v.) and clocinnamox (5 mg/kg s.c.) fully and persistently blocked the antinociception of a high dose of buprenorphine. An established effect of buprenorphine was less sensitive, although repeated administration of naloxone induced complete antagonism, as did the irreversible antagonist clocinnamox under prophylactic and curative treatment conditions. Our results suggest that the antinociceptive effect of buprenorphine is mainly, if not exclusively, mediated by activation of mu-opioid receptors. They confirm clinical experience that in the analgesic dose range a switch between buprenorphine and full mu-agonists is possible without loss of analgesic efficacy and without a refractory period between the termination of buprenorphine analgesia and the onset of action of the new mu-opioid treatment. Antinociception of buprenorphine is sensitive towards mu-opioid receptor antagonists and incomplete inhibition can be improved by increasing the dose or repetitive dosing.
Phenotypic markers and BCL-1 gene rearrangements in B-cell chronic lymphocytic leukemia: a Cancer and Leukemia Group B study (1993)

Abstract The markers, CD11b, CD11c, CD14, CD21, CD23, CD25, CD38, and FMC7 were correlated with morphologic and other laboratory and clinical characteristics of 127 patients with untreated CD5+ chronic lymphocytic leukemia (CLL). Only CD38 and CD21 were significantly associated with atypical CLL morphology. The integrin associated markers CD11b and CD11c were associated with lower leukocyte count (white blood cell count [WBC]) and lower Rai stage. By contrast, the activation antigen CD23 was associated with a higher WBC, higher Rai stage, younger age group, and the presence of lymphadenopathy. Therefore, we conclude that CD23 positivity may reflect a more aggressive form of CLL, and CD11b and CD11c positivity a less aggressive form. The BCL-1 gene rearrangement was present in 5 of 84 (6%) CLL cases examined and was associated with atypical morphology and surface expression of CD11b. Patients with a BCL-1 gene rearrangement may represent a CLL subset or possibly a different B-cell disease.
Integrins as Therapeutic Targets: Successes and Cancers (2017)

Integrins are transmembrane receptors that are central to the biology of many human pathologies. Classically mediating cell-extracellular matrix and cell-cell interaction, and with an emerging role as local activators of TGFβ, they influence cancer, fibrosis, thrombosis and inflammation. Their ligand binding and some regulatory sites are extracellular and sensitive to pharmacological intervention, as proven by the clinical success of seven drugs targeting them. The six drugs on the market in 2016 generated revenues of some US$3.5 billion, mainly from inhibitors of α4-series integrins. In this review we examine the current developments in integrin therapeutics, especially in cancer, and comment on the health economic implications of these developments.
Adeno-Associated Viral Vector Serotype 5 Poorly Transduces Liver in Rat Models (2013)

Preclinical studies in mice and non-human primates showed that AAV serotype 5 provides efficient liver transduction and as such seems a promising vector for liver directed gene therapy. An advantage of AAV5 compared to serotype 8 already shown to provide efficient correction in a phase 1 trial in patients suffering from hemophilia B, is its lower seroprevalence in the general population. Our goal is liver directed gene therapy for Crigler-Najjar syndrome type I, inherited severe unconjugated hyperbilirubinemia caused by UGT1A1 deficiency. In a relevant animal model, the Gunn rat, we compared the efficacy of AAV 5 and 8 to that of AAV1 previously shown to be effective. Ferrying a construct driving hepatocyte specific expression of UGT1A1, both AAV8 and AAV1 provided an efficient correction of hyperbilirubinemia. In contrast to these two and to other animal models AAV5 failed to provide any correction. To clarify whether this unexpected finding was due to the rat model used or due to a problem with AAV5, the efficacy of this serotype was compared in a mouse and two additional rat strains. Administration of an AAV5 vector expressing luciferase under the control of a liver specific promoter confirmed that this serotype poorly performed in rat liver, rendering it not suitable for proof of concept studies in this species.
A DISTORTION CORRECTION METHOD FOR ENDOSCOPE IMAGES BASED ON CALIBRATION PATTERNS AND A SIMPLE MATHEMATIC MODEL FOR OPTICAL LENS (2005)

In the past 30 years, the progress in optical engineering, computer science and electronic techniques have made the endoscopy an invaluable tool in both internal clinics and surgical operation. As its applications increase exponentially, it has even become a specialized division in the clinical medicine. In order to obtain a larger field of view inside a small and narrow gastrointestinal tract, an endoscope is usually equipped with a wide-angle lens (Fish eye lens). Thus, an acquired image is often with certain degree of shape distortion. The distortion gets even more serious as the objects extend outward from the center of the lens in radial. This paper discusses the effect of such distortion and the correction of the effect. By using a calibration pattern, the nonlinear distortion is corrected with a simple mathematic model for the endoscope image. Once the endoscopic lens is calibrated, the same mathematic model can be utilized repeatedly for the images captured by that endoscope. After capturing the calibration pattern using an endoscopic instrument, digital image processing techniques are applied to extract the calibration pattern from the distorted image. We propose a second order mathematic model and consider the parameters of optical lens. The coordinates of each dot in the calibration pattern are the input to the mathematic model for the correction of endoscope images. The experimental results show that the correction method is effective. For example, by comparing to the original calibration pattern image, the average errors in area calculation are 76.46% and 4.68% for the distorted and the corrected images, respectively.
Lipid-binding and antimicrobial properties of synthetic peptides of bovine apolipoprotein A-II (1999)

We previously showed that bovine apolipoprotein A-II (apoA-II) had antimicrobial activity against Escherichia coli and the yeast Saccharomyces cerevisiae in PBS. We have characterized here the active domain of apoA-II using synthetic peptides. A peptide corresponding to C-terminal residues Leu(49)-Thr(76) exhibited significant antimicrobial activity against E. coli in PBS, but not against S. cerevisiae. Experiments using amino-acid-substituted peptides indicated that the residues Phe(52)-Phe(53)-Lys(54)-Lys(55) are required for the activity. Peptide Leu(49)-Thr(76) induced the release of calcein trapped inside the vesicles whose lipid composition resembles that of E. coli membrane, suggesting that peptide Leu(49)-Thr(76) can destabilize the E. coli membrane. CD measurements showed that the alpha-helicity of peptide Leu(49)-Thr(76) increased from 3.5 to 36% by addition of the vesicles. When E. coli cells were incubated with peptide Leu(49)-Thr(76), some proteins were released to the external medium, probably owing to membrane destabilization caused by the peptide. In electron micrographs of E. coli cells treated with peptide Leu(49)-Thr(76), transparent nucleoids and granulated cytoplasm were observed. Amino acid substitutions, Phe(52)Phe(53)-->AlaAla (Phe(52, 53)-->Ala) in peptide Leu(49)-Thr(76) caused the loss of antimicrobial activity against E. coli, although protein-releasing activity was retained. Electron micrographs of the cells treated with peptide Leu(49)-Thr(76)(Phe(52,53)-->Ala) revealed morphological change only at the nucleoids. Therefore peptide Leu(49)-Thr(76) appears to primarily target the cytoplasm rather than the membrane of E. coli cells.
Biomarkers for Prostate Cancer (2008)

The development of biomarkers for prostate cancer screening, detection, and prognostication has revolutionized the management of this disease. Prostate-specific antigen (PSA) is a useful, though not specific, biomarker for detecting prostate cancer. We review the literature on prostate cancer biomarkers, including serum markers (PAP, tPSA, fPSA, proPSA, PSAD, PSAV, PSADT, EPCA, and EPCA-2), tissue markers (AMACR, methylated GSTP1, and the TMPRSS2-ETS gene rearrangement), and a urine marker (DD3PCA3/UPM-3). Future research should focus on validation of already existing biomarkers and the discovery of new markers to identify men with aggressive prostate cancer.
Fast and automated biomarker detection in breath samples with machine learning (2020)

Volatile organic compounds (VOCs) in human breath can reveal a large spectrum of health conditions and can be used for fast, accurate and non-invasive diagnostics. Gas chromatography-mass spectrometry (GC-MS) is used to measure VOCs, but its application is limited by expert-driven data analysis that is time-consuming, subjective and may introduce errors. We propose a system to perform GC-MS data analysis that exploits deep learning pattern recognition ability to learn and automatically detect VOCs directly from raw data, thus bypassing expert-led processing. The new proposed approach showed to outperform the expert-led analysis by detecting a significantly higher number of VOCs in just a fraction of time while maintaining high specificity. These results suggest that the proposed method can help the large-scale deployment of breath-based diagnosis by reducing time and cost, and increasing accuracy and consistency.
Odd-skipped related 1 is required for development of the metanephric kidney and regulates formation and differentiation of kidney precursor cells (2006)

Formation of kidney tissue requires the generation of kidney precursor cells and their subsequent differentiation into nephrons, the functional filtration unit of the kidney. Here we report that the gene odd-skipped related 1 (Odd1) plays an important role in both these processes. Odd1 is the earliest known marker of the intermediate mesoderm, the precursor to all kidney tissue. It is localized to mesenchymal precursors within the mesonephric and metanephric kidney and is subsequently downregulated upon tubule differentiation. Mice lacking Odd1 do not form metanephric mesenchyme, and do not express several other factors required for metanephric kidney formation, including Eya1, Six2, Pax2, Sall1 and Gdnf. In transient ectopic expression experiments in the chick embryo, Odd1 can promote expression of the mesonephric precursor markers Pax2 and Lim1. Finally, persistent expression of Odd1 in chick mesonephric precursor cells inhibits differentiation of these precursors into kidney tubules. These data indicate that Odd1 plays an important role in establishing kidney precursor cells, and in regulating their differentiation into kidney tubular tissue.
Criticality-Aware Dynamic Task Scheduling for Heterogeneous Architectures (2015)

Current and future parallel programming models need to be portable and efficient when moving to heterogeneous multi-core systems. OmpSs is a task-based programming model with dependency tracking and dynamic scheduling. This paper describes the OmpSs approach on scheduling dependent tasks onto the asymmetric cores of a heterogeneous system. The proposed scheduling policy improves performance by prioritizing the newly-created tasks at runtime, detecting the longest path of the dynamic task dependency graph, and assigning critical tasks to fast cores. While previous works use profiling information and are static, this dynamic scheduling approach uses information that is discoverable at runtime which makes it implementable and functional without the need of an oracle or profiling. The evaluation results show that our proposal outperforms a dynamic implementation of Heterogeneous Earliest Finish Time by up to 1.15x, and the default breadth-first OmpSs scheduler by up to 1.3x in an 8-core heterogeneous platform and up to 2.7x in a simulated 128-core chip.
Call/Messaging Open API for Telecommunication Services (2008)

With the saturation of existing intelligent network services, it is becoming increasingly difficult to develop new profitable services. The current trend seems to be moving toward the convergence of traditional telephone networks with the Internet. The capabilities of Internet terminals, such as PCs, are more powerful than those of traditional terminals for telephone networks, particularly in terms of their storage capabilities and user interface. IT developers can easily create new telecommunication services using Parlay APIs, without needing to become experts in the field of telephony. Although using SOAP over HTTP allows for easier communication, normal individual developers have some difficulties in processing SOAP messages due to the verbose XML format. REST based APIs can be a good alternative, as they have no additional messaging layer except for HTTP. In this paper, we introduce REST based Open APIs for building outbound call and messaging services. The suggested APIs enable the service features of click-to-dial, mini-conference, call record, audio-on-demand, short messaging and voice messaging, and show the power of the convergence between telephone networks and the internet.
Bypassing vocoders in CDMA mobile-to-mobile calls (2002)

In present-day CDMA networks, interconnection of mobile switching centers (MSCs) results in a mobile-to-mobile call typically being processed by the vocoder twice, once for mobile-to-land transmission and again for the land-to-mobile portion of the call. Bypassing vocoders in CDMA mobile-to-mobile calls will improve the voice quality and increase the subscriber serving capacity of the base station controller (BSC) and MSC, providing an evolutionary step towards the open and flexible architecture for next generation wireless networks. To bypass vocoders in CDMA mobile-to-mobile calls, this paper proposes interconnecting BSCs via an ATM network using AAL2, complementing the effort to interconnect wireless network components with ATM networks to provide a high-speed backbone. The use of AAL2 is recommended because of the bandwidth efficiency it can achieve with the given transmission of low-rate, short, and variable length packets in a delay-sensitive application. This paper discusses the setup procedure of a mobile-to-mobile call that bypasses the vocoder. We simulated the delivery of mobile-to-mobile calls over AAL2 to study the impact of GCRA traffic policing and cell spacer traffic shaping on the ATM network based inter-BSC connection.
List decoding for nested lattices and applications to relay channels (2010)

We demonstrate a decoding scheme for nested lattice codes which is able to decode a list of a particular size which contains the transmitted codeword with high probability. This list decoder is analogous to that used in random coding arguments in achievability schemes of relay channels, and allows for the effective combination of information from the relay and source node. Using this list decoding result, we demonstrate 1) that lattice codes may achieve the capacity of the physically degraded AWGN relay channel, 2) an achievable rate region for the two-way relay channel with direct links using lattice codes, and 3) that we may improve the constant gap to capacity for specific cases of the two-way relay channel with direct links.
Management of the Diabetic Patient with Advanced Chronic Kidney Disease (2010)

Diabetic kidney disease (DKD) is the leading cause of end-stage renal disease (ESRD), and one of the most prevalent microvascular complications of both type 1 and type 2 diabetes. Additionally, risk of death is increased at all stages of DKD. As early as the microalbuminuric stage, the death rate approaches 20% per year. Therefore, management strategies should address reducing risk of mortality as well as progression to ESRD. DKD is associated with multiple co-morbidities including hypertension, dyslipidemia, cardiovascular disease, anemia, and bone and mineral metabolism disorders (BMD). Anemia and BMD often occur earlier in the course of DKD than with other forms of chronic kidney disease. Pharmacological and dietary management of hyperglycemia, hypertension, dyslipidemia, anemia, and BMD pose specific challenges in DKD. However, with heightened awareness of risks and a multifactorial management approach, the impact of DKD on micro- and macrovascular complications and death can be reduced.