gebhart/patrepeval huggingface dataset:
Imaging spatial heterodyne spectroscopy: theory and practice (1999)

Spatial heterodyne spectroscopy (SHS) is a Fourier transform spectroscopy technique capable of very high spectral resolution with no moving parts. The original work described non-imaging SHS, and it became a true imaging spectroscopy technique without much fanfare. We describe the imaging technique and relate it to another 'image plane interferometer' described by Horton, called HEIFTS, which does not have heterodyned fringes. One configuration of a basic SHS is a two-beam Michelson interferometer with both mirrors replace by diffraction gratings operated in the Littrow configuration. To convert a parallel light SHS device to imaging, incoming light must be focused on the gratings, so that each grating receives a full image of the scene. To acquire 3D data cubes, the open field of view is scanned across the scene. Although the focal plane array sees both spatial and spectral information, they are not mixed, because information is encoded by optical path difference according to position on the focal plane.
PD-L1 expression in human cancers and its association with clinical outcomes (2016)

PD-L1 is an immunoinhibitory molecule that suppresses the activation of T cells, leading to the progression of tumors. Overexpression of PD-L1 in cancers such as gastric cancer, hepatocellular carcinoma, renal cell carcinoma, esophageal cancer, pancreatic cancer, ovarian cancer, and bladder cancer is associated with poor clinical outcomes. In contrast, PD-L1 expression correlates with better clinical outcomes in breast cancer and merkel cell carcinoma. The prognostic value of PD-L1 expression in lung cancer, colorectal cancer, and melanoma is controversial. Blocking antibodies that target PD-1 and PD-L1 have achieved remarkable response rates in cancer patients who have PD-L1-overexpressing tumors. However, using PD-L1 as an exclusive predictive biomarker for cancer immunotherapy is questionable due to the low accuracy of PD-L1 immunohistochemistry staining. Factors that affect the accuracy of PD-L1 immunohistochemistry staining are as follows. First, antibodies used in different studies have different sensitivity. Second, in different studies, the cut-off value of PD-L1 staining positivity is different. Third, PD-L1 expression in tumors is not uniform, and sampling time and location may affect the results of PD-L1 staining. Therefore, better understanding of tumor microenvironment and use of other biomarkers such as gene marker and combined index are necessary to better identify patients who will benefit from PD-1/PD-L1 checkpoint blockade therapy.
HRAS1-selected chromosome transfer generates markers that colocalize aniridia- and genitourinary dysplasia-associated translocation breakpoints and the Wilms tumor gene within band 11p13. (1987)

We show that chromosome-mediated gene transfer can provide an enriched source of DNA markers for predetermined, subchromosomal regions of the human genome. Forty-four human DNA recombinants isolated from a HRAS1-selected chromosome-mediated gene transformant map exclusively to chromosome 11, with several sublocalizing to the Wilms tumor region at 11p13. We present a detailed molecular map of the deletion chromosomes 11 from five WAGR (Wilms tumor/aniridia/genitourinary abnormalities/mental retardation) syndrome patients, three of which are at the limits of cytogenetic resolution but shown here to be molecularly distinguishable and overlapping. We can define ten distinct regions of the short arm of chromosome 11, five of which subdivide band 11p13. We also map two independent 11p13 translocation breakpoints to within the smallest region of overlap defined by the WAGR deletions. The first comes from a patient with familial aniridia, and the second from a patient with Potter facies and genitourinary dysplasia. The close similarities in map location and affected cell lineage for Wilms tumor and genitourinary dysplasia suggest that they may be alternative manifestations of mutation at the same locus.
Algorithms for Arabic name transliteration (1994)

An Arabic name can be written in English with many different spellings. For example, the name Sulayman is written only one way in Arabic. In English, this name is written in as many as forty different ways, such as Salayman, Seleiman, Solomon, Suleiman, and Sylayman. Currently, Arabic linguists manually transliterate these names—a slow, laborious, error-prone, and time-consuming process. We present a hybrid algorithm which automates this process in real time using neural networks and a knowledge-based system to vowelize Arabic. A supervised neural network filters out unreliable names, passing the reliable names on to the knowledge-based system for romanization. This approach, developed at the IBM Federal Systems Company, is applicable to a wide variety of purposes, including visa processing and document processing by border patrols.
Quantum thermalization through entanglement in an isolated many-body system (2016)

Statistical mechanics relies on the maximization of entropy in a system at thermal equilibrium. However, an isolated quantum many-body system initialized in a pure state remains pure during Schrödinger evolution, and in this sense it has static, zero entropy. We experimentally studied the emergence of statistical mechanics in a quantum state and observed the fundamental role of quantum entanglement in facilitating this emergence. Microscopy of an evolving quantum system indicates that the full quantum state remains pure, whereas thermalization occurs on a local scale. We directly measured entanglement entropy, which assumes the role of the thermal entropy in thermalization. The entanglement creates local entropy that validates the use of statistical physics for local observables. Our measurements are consistent with the eigenstate thermalization hypothesis.
Property-based testing (1997)

The goal of software testing analysis is to validate that an implementation satisfies its specifications. Many errors in software are caused by generalizable flaws in the source code. Property-based testing assures that a given program is free of specified generic flaws. Property-based testing uses property specifications and a data-flow analysis of the program to guide evaluation of test executions for correctness and completeness.
c-Abl Has High Intrinsic Tyrosine Kinase Activity That Is Stimulated by Mutation of the Src Homology 3 Domain and by Autophosphorylation at Two Distinct Regulatory Tyrosines (2000)

Using the specific Abl tyrosine kinase inhibitor STI 571, we purified unphosphorylated murine type IV c-Abl and measured the kinetic parameters of c-Abl tyrosine kinase activity in a solution with a peptide-based assay. Unphosphorylated c-Abl exhibited substantial peptide kinase activity with K(m) of 204 microm and V(max) of 33 pmol min(-1). Contrary to previous observations using immune complex kinase assays, we found that a transforming c-Abl mutant with a Src homology 3 domain point mutation (P131L) had significantly (about 6-fold) higher intrinsic kinase activity than wild-type c-Abl (K(m) = 91 microm, V(max) = 112 pmol min(-1)). Autophosphorylation stimulated the activity of wild-type c-Abl about 18-fold and c-Abl P131L about 3.6-fold, resulting in highly active kinases with similar catalytic rates. The autophosphorylation rate was dependent on Abl protein concentration consistent with an intermolecular reaction. A tyrosine to phenylalanine mutation (Y412F) at the c-Abl residue homologous to the c-Src catalytic domain autophosphorylation site impaired the activation of wild-type c-Abl by 90% but reduced activation of c-Abl P131L by only 45%. Mutation of a tyrosine (Tyr-245) in the linker region between the Src homology 2 and catalytic domains that is conserved among the Abl family inhibited the autophosphorylation-induced activation of wild-type c-Abl by 50%, whereas the c-Abl Y245F/Y412F double mutant was minimally activated by autophosphorylation. These results support a model where c-Abl is inhibited in part through an intramolecular Src homology 3-linker interaction and stimulated to full catalytic activity by sequential phosphorylation at Tyr-412 and Tyr-245.
Human Relaxin Gene 3 (H3) and the Equivalent Mouse Relaxin (M3) Gene (2002)

We have identified a novel human relaxin gene, designated H3 relaxin, and an equivalent relaxin gene in the mouse from the Celera Genomics data base. Both genes encode a putative prohormone sequence incorporating the classic two-chain, three cysteine-bonded structure of the relaxin/insulin family and, importantly, contain the RXXXRXX(I/V) motif in the B-chain that is essential for relaxin receptor binding. A peptide derived from the likely proteolytic processing of the H3 relaxin prohormone sequence was synthesized and found to possess relaxin activity in bioassays utilizing the human monocytic cell line, THP-1, that expresses the relaxin receptor. The expression of this novel relaxin gene was studied in mouse tissues using RT-PCR, where transcripts were identified with a pattern of expression distinct from that of the previously characterized mouse relaxin. The highest levels of expression were found in the brain, whereas significant expression was also observed in the spleen, thymus, lung, and ovary. Northern blotting demonstrated an approximately 1.2-kb transcript present in mouse brain poly(A) RNA but not in other tissues. These data, together with the localization of transcripts in the pars ventromedialis of the dorsal tegmental nucleus of C57BLK6J mouse brain by in situ hybridization histochemistry, suggest a new role for relaxin in neuropeptide signaling processes. Together, these studies describe a third member of the human relaxin family and its equivalent in the mouse.
Autophagy in pancreatic cancer (2010)

Pancreatic cancer, the fourth leading cause of cancer-related death in the United States, is resistant to current chemotherapies. Therefore, identification of different pathways of cell death is important to develop novel therapeutics. Our previous study has shown that triptolide, a diterpene triepoxide, inhibits the growth of pancreatic cancer cells in vitro and prevents tumor growth in vivo. However, the mechanism by which triptolide kills pancreatic cancer cells was not known, hence, this study aimed at elucidating it. Our study reveals that triptolide kills diverse types of pancreatic cancer cells by two different pathways; it induces caspase-dependent apoptotic death in some cell lines and death via a caspase-independent autophagic pathway in the other cell lines tested. Triptolide-induced autophagy requires autophagy-specific genes, atg5 or beclin 1 and its inhibition results in cell death via the apoptotic pathway, whereas inhibition of both autophagy and apoptosis rescues triptolide-mediated cell death. Our study shows for the first time that induction of autophagy by triptolide has a pro-death role in pancreatic cancer cells. Since triptolide kills diverse pancreatic cancer cells by different mechanisms, it makes an attractive chemotherapeutic agent for future use against a broad spectrum of pancreatic cancers.
Nanoscale Molecular Traps and Dams for Ultrafast Protein Enrichment in High-Conductivity Buffers (2012)

We report a new approach, molecular dam, to enhance mass transport for protein enrichment in nanofluidic channels by nanoscale electrodeless dielectrophoresis under physiological buffer conditions. Dielectric nanoconstrictions down to 30 nm embedded in nanofluidic devices serve as field-focusing lenses capable of magnifying the applied field to 10(5)-fold when combined with a micro- to nanofluidic step interface. With this strong field and the associated field gradient at the nanoconstrictions, proteins are enriched by the molecular damming effect faster than the trapping effect, to >10(5)-fold in 20 s, orders of magnitude faster than most reported methods. Our study opens further possibilities of using nanoscale molecular dams in miniaturized sensing platforms for rapid and sensitive protein analysis and biomarker discovery, with potential applications in precipitation studies and protein crystallization and possible extensions to small-molecules enrichment or screening.
Fourier domain mode locked lasers for OCT imaging at up to 290 kHz sweep rates (2005)

A high speed, tunable laser using Fourier Domain Mode Locking is demonstrated for OCT imaging. Record sweep speeds up to 290 kHz, 3 cm coherence length and 145 nm range at 1300 nm are achieved.
Novel composite organic–inorganic semiconductor sensors for the quantitative detection of target organic vapours (1996)

Composites of tin dioxide (an n-type semiconductor) and derivatives of the conducting polymer polypyrrole (a p-type semiconductor) gave reversible changes in electrical resistance at room temperature when exposed to a range of organic vapours. The optimum amount of polymer giving highest sensitivity was found by experiment to be 2.5% by mass for the polypyrrole chloride-tin dioxide composite. Composites containing 2.5% polymer by mass but differing in polymer derivative, were fabricated and exposed to low concentrations of ethanol, methanol, acetone, methyl acetate and ethyl acetate. All were found to give significant and reversible decreases in electrical resistance. Direct comparison with sensors constructed solely of tin dioxide or polypyrrole at room temperature showed the composites to be more sensitive. The gas sensitivity of the composite materials depended on the type of polymer derivative incorporated and the dopant anion associated with the polymer. The composites were simple to fabricate and gave differing response profiles to a range of organic vapours.
Temperature, Crystalline Phase and Influence of Substrate Properties in Intense Pulsed Light Sintering of Copper Sulfide Nanoparticle Thin Films (2018)

Intense Pulsed Light sintering (IPL) uses pulsed, visible light to sinter nanoparticles (NPs) into films used in functional devices. While IPL of chalcogenide NPs is demonstrated, there is limited work on prediction of crystalline phase of the film and the impact of optical properties of the substrate. Here we characterize and model the evolution of film temperature and crystalline phase during IPL of chalcogenide copper sulfide NP films on glass. Recrystallization of the film to crystalline covellite and digenite phases occurs at 126 °C and 155 °C respectively within 2-7 seconds. Post-IPL films exhibit p-type behavior, lower resistivity (~10<sup>-3</sup>-10<sup>-4</sup> Ω-cm), similar visible transmission and lower near-infrared transmission as compared to the as-deposited film. A thermal model is experimentally validated, and extended by combining it with a thermodynamic approach for crystal phase prediction and via incorporating the influence of film transmittivity and optical properties of the substrate on heating during IPL. The model is used to show the need to a-priori control IPL parameters to concurrently account for both the thermal and optical properties of the film and substrate in order to obtain a desired crystalline phase during IPL of such thin films on paper and polycarbonate substrates.
Toward high communication performance through compiled communications on a circuit switched interconnection network (2002)

This paper discusses a new principle of interconnection network for massively parallel architectures in the field of numerical computation. The principle is motivated by an analysis of the application features and the need to design new kind of communication networks combining very high bandwidth, very low latency, performance independence to communication pattern or network load and a performance improvement proportional to the hardware performance improvement. Our approach is to associate compiled communications and a circuit switched interconnection network. This paper presents the motivations for this principle, the hardware and software issues and the design of a first prototype. The expected performance are a sustained aggregate bandwidth of more than 500 GBytes/s and an overall latency less than 270 ns, for a large implementation (4K inputs) with the current available technology.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Defective Lipoprotein Receptors and Atherosclerosis (1983)

In 1913, Anitschkow fed cholesterol to rabbits, and thereby demonstrated that a high blood level of cholesterol can produce atherosclerosis in animals just as it can in human beings — with one fundamental difference. Human hypercholesterolemia is caused by genetic or acquired abnormalities in the synthesis or degradation of plasma lipoproteins that shuttle endogenous cholesterol between body tissues; dietary cholesterol is only an indirect aggravating factor. In laboratory animals hypercholesterolemia is produced exogenously when the normal mechanisms of lipoprotein clearance are overwhelmed by large amounts of dietary cholesterol. Since dietary and endogenous cholesterol are transported by different plasma lipoproteins, the . . .
Hematopoietic cytokines (2008)

The production of hematopoietic cells is under the tight control of a group of hematopoietic cytokines. Each cytokine has multiple actions mediated by receptors whose cytoplasmic domains contain specialized regions initiating the various responses-survival, proliferation, differentiation commitment, maturation, and functional activation. Individual cytokines can be lineage specific or can regulate cells in multiple lineages, and for some cell types, such as stem cells or megakaryocyte progenitors, the simultaneous action of multiple cytokines is required for proliferative responses. The same cytokines control basal and emergency hematopoietic cell proliferation. Three cytokines, erythropoietin, granulocyte colony-stimulating factor, and granulocyte-macrophage colony-stimulating factor, have now been in routine clinical use to stimulate cell production and in total have been used in the management of many millions of patients. In this little review, discussion will be restricted to those cytokines well established as influencing the production of hematopoietic cells and will exclude newer candidate regulators and those active on lymphoid cells. As requested, this account will describe the cytokines in a historical manner, using a sequential format of discovery, understanding, validation, and puzzlement, a sequence that reflects the evolving views on these cytokines over the past 50 years.
Effects of acute renal failure on the pharmacokinetics of DA‐7867, a new oxazolidinone, in rats (2005)

The pharmacokinetic parameters of DA-7867 were compared after intravenous and oral administration at a dose of 10 mg/kg to control rats and rats with acute renal failure induced by uranyl nitrate (rats with U-ARF). After intravenous administration in rats with U-ARF, the time-averaged total body clearance (Cl) was significantly faster (2.45 versus 0.932 ml/min/kg) than controls due to significantly faster nonrenal clearance (2.25 versus 0.855 ml/min/kg) in rats with U-ARF. The faster nonrenal clearance could be due to significantly greater gastrointestinal (including biliary) excretion; the amount of unchanged DA-7867 recovered from the entire gastrointestinal tract at 24 h was significantly greater (30.3% versus 9.38% of intravenous dose) in rats with U-ARF. In rats with U-ARF, the Vss was significantly larger (1420 ml/kg compared with 580 ml/kg), but this was not due to a difference in plasma protein binding; the values were comparable between the two groups of rats. After oral administration to rats with U-ARF, the total area under the plasma concentration-time from time zero to time infinity (AUC) of DA-7867 was significantly smaller than the controls (2560 microg min/ml versus 7440 microg min/ml), and this was not due mainly to a decrease in absorption from the gastrointestinal tract in rats with U-ARF.
Formation and Persistence of Isoniazid-DNA Adducts in Mouse Tissues (1987)

Further confirmation is provided to support the identity of the product formed by the in vitro reaction of isoniazid (INH) with cytosine as 4-deamino-4-isoniazidocytosine (INH-cytosine). Use of INH-treated mice, in which the tissue DNA is prelabelled by the neonatal administration of [3H]-deoxycytidine, has revealed the presence of two other DNA products in addition to INH-cytosine. Tissue differences in the persistence of these three DNA products suggest the presence of repair reactions for certain adducts. These processes and the effects of hepatotoxicity lead to a selective retention of adducts in the DNA of lung which is the target tissue for INH-carcinogenicity in mice. INH-modified DNA templates are weakly promutagenic during in vitro DNA synthesis. The implications of these observations for the role of INH as an initiating agent and for the species differences in its carcinogenicity are discussed.
Large-scale cluster management at Google with Borg (2015)

Google's Borg system is a cluster manager that runs hundreds of thousands of jobs, from many thousands of different applications, across a number of clusters each with up to tens of thousands of machines.
Caspase Family Proteases and Apoptosis (2005)

Apoptosis, or programmed cell death, is an essential physiological process that plays a critical role in development and tissue homeostasis. The progress of apoptosis is regulated in an orderly way by a series of signal cascades under certain circumstances. The caspase-cascade system plays vital roles in the induction, transduction and amplification of intracellular apoptotic signals. Caspases, closely associated with apoptosis, are aspartate-specific cysteine proteases and members of the interleukin-1beta-converting enzyme family. The activation and function of caspases, involved in the delicate caspase-cascade system, are regulated by various kinds of molecules, such as the inhibitor of apoptosis protein, Bcl-2 family proteins, calpain, and Ca2+. Based on the latest research, the members of the caspase family, caspase-cascade system and caspase-regulating molecules involved in apoptosis are reviewed.
Consistent Recovery of Sensory Stimuli Encoded with MIMO Neural Circuits (2009)

We consider the problem of reconstructing finite energy stimuli encoded with a population of spiking leaky integrate-and-fire neurons. The reconstructed signal satisfies a consistency condition: when passed through the same neuron, it triggers the same spike train as the original stimulus. The recovered stimulus has to also minimize a quadratic smoothness optimality criterion. We formulate the reconstruction as a spline interpolation problem for scalar as well as vector valued stimuli and show that the recovery has a unique solution. We provide explicit reconstruction algorithms for stimuli encoded with single as well as a population of integrate-and-fire neurons. We demonstrate how our reconstruction algorithms can be applied to stimuli encoded with ON-OFF neural circuits with feedback. Finally, we extend the formalism to multi-input multi-output neural circuits and demonstrate that vector-valued finite energy signals can be efficiently encoded by a neural population provided that its size is beyond a threshold value. Examples are given that demonstrate the potential applications of our methodology to systems neuroscience and neuromorphic engineering.