gebhart/patrepeval huggingface dataset:
Cell-specific expression and pathway analyses reveal alterations in trauma-related human T cell and monocyte pathways (2006)

Monitoring genome-wide, cell-specific responses to human disease, although challenging, holds great promise for the future of medicine. Patients with injuries severe enough to develop multiple organ dysfunction syndrome have multiple immune derangements, including T cell apoptosis and anergy combined with depressed monocyte antigen presentation. Genome-wide expression analysis of highly enriched circulating leukocyte subpopulations, combined with cell-specific pathway analyses, offers an opportunity to discover leukocyte regulatory networks in critically injured patients. Severe injury induced significant changes in T cell (5,693 genes), monocyte (2,801 genes), and total leukocyte (3,437 genes) transcriptomes, with only 911 of these genes common to all three cell populations (12%). T cell-specific pathway analyses identified increased gene expression of several inhibitory receptors (PD-1, CD152, NRP-1, and Lag3) and concomitant decreases in stimulatory receptors (CD28, CD4, and IL-2Ralpha). Functional analysis of T cells and monocytes confirmed reduced T cell proliferation and increased cell surface expression of negative signaling receptors paired with decreased monocyte costimulation ligands. Thus, genome-wide expression from highly enriched cell populations combined with knowledge-based pathway analyses leads to the identification of regulatory networks differentially expressed in injured patients. Importantly, application of cell separation, genome-wide expression, and cell-specific pathway analyses can be used to discover pathway alterations in human disease.
Introduction to Algorithms, third edition (2009)

If you had to buy just one text on algorithms, Introduction to Algorithms is a magnificent choice. The book begins by considering the mathematical foundations of the analysis of algorithms and maintains this mathematical rigor throughout the work. The tools developed in these opening sections are then applied to sorting, data structures, graphs, and a variety of selected algorithms including computational geometry, string algorithms, parallel models of computation, fast Fourier transforms (FFTs), and more. This book's strength lies in its encyclopedic range, clear exposition, and powerful analysis. Pseudo-code explanation of the algorithms coupled with proof of their accuracy makes this book is a great resource on the basic tools used to analyze the performance of algorithms.
Review Article: A new wrinkle on old skin: the role of elastic fibres in skin ageing (2010)

Cutaneous ageing is the result of two distinct, biological processes which may occur concurrently: (i) the passage of time, termed intrinsic ageing and (ii) environmental influences, termed extrinsic ageing. Intrinsic ageing of the skin is a slow process which causes changes in tissue structure and impairs function in the absence of additional biological, chemical and physical factors. The clinical features of intrinsically aged skin are not usually evident until old age when, although smooth and unblemished, the skin surface appears pale and is characterized by fine wrinkles with occasional exaggerated expression lines. Functionally, intrinsically aged skin is dry and less elastic than more youthful skin. In contrast, extrinsically aged skin is exemplified by deep, coarse wrinkles, mottled hyperpigmentation and a marked loss of elasticity and recoil. The two major environmental influences which induce extrinsic ageing are: (i) chronic exposure to solar ultraviolet (UV) irradiation (termed photoageing) and (ii) smoking. This review discusses the changes associated with the ageing process in the skin, with particular emphasis on the role played by the elastic fibre network in maintaining dermal function. The review concludes with a discussion of a short-term assay for independent assessment of the efficacy of anti-ageing cosmetic products using the elastic fibre component fibrillin-1 as a biomarker of extracellular matrix repair.
<title>Speckle interferometry in the measurements of biotissue vibrations</title> (1992)

The mechanism of speckle interferometer output signal forming for biovibration measurements is discussed. Statistical characteristics analysis of output signal amplitude is carried out. The factors creating parasitic amplitude-phase modulation of the output signal are investigated. The possibility of differential homodyne speckle interferometers application in Tibetan pulse diagnostics is shown.
Cloning and Characterization of MEK6, a Novel Member of the Mitogen-activated Protein Kinase Kinase Cascade (1996)

Mitogen-activated protein kinases are members of a conserved cascade of kinases involved in many signal transduction pathways. They stimulate phosphorylation of transcription factors in response to extracellular signals such as growth factors, cytokines, ultraviolet light, and stress-inducing agents. A novel mitogen-activated protein kinase kinase, MEK6, was cloned and characterized. The complete MEK6 cDNA was isolated by polymerase chain reaction. It encodes a 334-amino acid protein with 82% identity to MKK3. MEK6 is highly expressed in skeletal muscle like many other members of this family, but in contrast to MKK3 its expression in leukocytes is very low. MEK6 is a member of the p38 kinase cascade and efficiently phosphorylates p38 but not c-Jun N-terminal kinase (JNK) and extracellular signal-regulated kinase (ERK) family members in direct kinase assays. Coupled kinase assays demonstrated that MEK6 induces phosphorylation of ATF2 by p38 but does not phosphorylate ATF2 directly. MEK6 is strongly activated by UV, anisomycin, and osmotic shock but not by phorbol esters, nerve growth factor, and epidermal growth factor. This separates MEK6 from the ERK subgroup of protein kinases. MEK6 is only a poor substrate for MEKK, a mitogen-activated protein kinase kinase kinase that efficiently phosphorylates the related family member JNKK.
<title>Complexity and performance of on-chip biochemical assays</title> (1997)

The use of microchips for performing biochemical processes has the potential to reduce reagent use and thus assay costs, increase throughput, and automate complex processes. We are building a multifunctional platform that provides sensing and actuation functions for a variety of microchip- based biochemical and analytical processes. Here we describe recent experiments that include on-chip dilution, reagent mixing, reaction, separation, and detection for important classes of biochemical assays. Issues in chip design and control are discussed.
Discovery of Type II Inhibitors of TGFβ-Activated Kinase 1 (TAK1) and Mitogen-Activated Protein Kinase Kinase Kinase Kinase 2 (MAP4K2) (2014)

We developed a pharmacophore model for type II inhibitors that was used to guide the construction of a library of kinase inhibitors. Kinome-wide selectivity profiling of the library resulted in the identification of a series of 4-substituted 1H-pyrrolo[2,3-b]pyridines that exhibited potent inhibitory activity against two mitogen-activated protein kinases (MAPKs), TAK1 (MAP3K7) and MAP4K2, as well as pharmacologically well interrogated kinases such as p38α (MAPK14) and ABL. Further investigation of the structure-activity relationship (SAR) resulted in the identification of potent dual TAK1 and MAP4K2 inhibitors such as 1 (NG25) and 2 as well as MAP4K2 selective inhibitors such as 16 and 17. Some of these inhibitors possess good pharmacokinetic properties that will enable their use in pharmacological studies in vivo. A 2.4 Å cocrystal structure of TAK1 in complex with 1 confirms that the activation loop of TAK1 assumes the DFG-out conformation characteristic of type II inhibitors.
FLICE Is Predominantly Expressed as Two Functionally Active Isoforms, Caspase-8/a and Caspase-8/b (1997)

Induction of apoptosis by the cell surface receptor CD95 (APO-1/Fas) has been shown to involve activation of a family of cysteine proteases (caspases). Recently, a new member of this family has been identified, designated FLICE (caspase-8/MACH/Mch5). FLICE is part of the CD95 death-inducing signaling complex and is therefore the most upstream caspase in the CD95 apoptotic pathway. A total of eight different isoforms of FLICE (caspase-8/a-h) have been described. To determine which isoforms are expressed in different cells we have generated a panel of monoclonal antibodies directed against all functional domains of FLICE. Using these antibodies we could show that only two of the FLICE isoforms (caspase-8/a and caspase-8/b) were predominantly expressed in cells of different origin. Both isoforms were recruited to the CD95 death-inducing signaling complex and were activated upon CD95 stimulation with similar kinetics. Taken together, only two of the eight published caspase-8 isoforms could be detected in significant amounts at the protein level.
Storage Management for Files of Dynamic Records. (1993)

We propose a new scheme for managing files of variable-length dynamic records, based on storing the records in large, fixed-length blocks. We demonstrate the e#ectiveness of this scheme for text indexing, showing that it achieves space utilisation of over 95%. With an appropriate block size and caching strategy, our scheme requires on average around two disk accesses---one read and one write---for insertion of or change to a record.
Phosphorus‐Doped Polycrystalline Silicon via LPCVD: I . Process Characterization (1984)

We have studied the low pressure chemical vapor deposition (LPCVD) process as applied to the preparation of in situ phosphorus‐doped polycrystalline silicon films. Thickness profiling, electron microprobe, and mass spectrometry have been utilized in the characterization of this process. The addition of phosphine as the dopant bearing precursor molecule was found to result in a factor of 25 decay in film growth rates relative to the intrinsic LPCVD process. The physical and chemical characteristics of samples prepared in this manner are shown to be a strong function of local reactor geometry, with growth‐rate variations of a factor of two within a wafer commonly observed. Mass spectrometry data is presented supporting the proposal that phosphine passivates the silicon surface, and the implications of this phenomenon for altering silicon growth kinetics are discussed. A model is presented accounting for the growth‐rate variations observed within individual wafers, as well as for the sensitivity of the phosphine‐doped process to system geometry.
Synthesis of high-temperature CO2 adsorbents from organo-layered double hydroxides with markedly improved CO2 capture capacity (2012)

Synthesis of highly efficient high-temperature CO2 adsorbents from organo-layered double hydroxides (LDHs) is presented for the first time. We demonstrate that the intercalation of long carbon-chain organic anions markedly increases the CO2 capture capacity (1.25 mmol g−1), 2.5 times higher than that of traditional adsorbents (0.5 mmol g−1). This work suggests a new direction for the synthesis of high-temperature CO2 adsorbents.
Domain adaptation for statistical machine translation with monolingual resources (2009)

Domain adaptation has recently gained interest in statistical machine translation to cope with the performance drop observed when testing conditions deviate from training conditions. The basic idea is that in-domain training data can be exploited to adapt all components of an already developed system. Previous work showed small performance gains by adapting from limited in-domain bilingual data. Here, we aim instead at significant performance gains by exploiting large but cheap monolingual in-domain data, either in the source or in the target language. We propose to synthesize a bilingual corpus by translating the monolingual adaptation data into the counterpart language. Investigations were conducted on a state-of-the-art phrase-based system trained on the Spanish--English part of the UN corpus, and adapted on the corresponding Europarl data. Translation, re-ordering, and language models were estimated after translating in-domain texts with the baseline. By optimizing the interpolation of these models on a development set the BLEU score was improved from 22.60% to 28.10% on a test set.
Stories of Resistance (2005)

Abstract This study explores the ways that women are shaped by hearing and telling stories of resistance to violence. By examining the narratives of women discussing stories of resistance, this analysis treats resistance as forms of resilience and empowerment that women knit together to create lives free of abuse. This research suggests that women view themselves as actively working to create violence-free relationships, that women's construction of violence resistant identities often grows from small acts, and that shared stories of resistance serve as powerful resources to help women avoid or leave abusive relationships.
Fine-needle aspiration biopsy of metastatic small cell carcinoma from extrapulmonary sites (1998)

Like a pulmonary counterpart, extrapulmonary small cell carcinoma (SCC) is an aggressive tumor with a high rate of metastasis. Forty-nine fine-needle aspiration biopsies (FNABs) (36 patients) of various primary sites other than the lung diagnosed as metastatic SCC (including Merkel cell carcinoma) were reviewed. FNABs were derived from lymph nodes (20), liver (7), bone (2), breast (1), pancreas (1), and skin/soft tissue (18). Primary tumor sites included the prostate (14), skin (11; Merkel cell carcinoma), cervix (5), urinary bladder (3), urethra (1), ovary (1), and parotid (1). Aspirates revealed predominantly dispersed single tumor cells with occasional clustering. Tumor cells were small with scant cytoplasm, fine powdery chromatin, and inconspicuous nucleoli. Nuclear molding, mitotic figures, and apoptotic bodies were frequently observed. In four cases, findings from the FNABs were used to render the initial diagnosis of SCC. FNAB is useful for determining whether metastases contain a SCC component, a finding that may alter clinical management. Cytologically, SCC from different primary sites cannot be differentiated, and its distinction requires clinical and radiographic correlation.
Total synthesis and expression of a gene for the α-subunit of bovine rod outer segment guanine nucleotide-binding protein (transducin) (1988)

To facilitate structure-function studies by site-specific mutagenesis, we have synthesized a gene for the alpha-subunit of the bovine rod outer segment (ROS) guanine nucleotide-binding protein (transducin). The gene codes for the native amino acid sequence and contains, by design, 38 unique restriction sites which are uniformly spaced. This enables mutagenesis in any part of the gene by restriction fragment replacement. The gene is 1076 base pairs in length. It was constructed from 44 synthetic oligonucleotides which were joined enzymatically in vitro into four fragments which were cloned. The synthetic transducin gene and cDNA encoding transducin were expressed to similar levels in monkey kidney cells (COS-1) using a vector in which transcription was under the control of the adenovirus major late promoter.
THE SYNTHESIS OF BILIRUBIN GLUCURONIDE BY TISSUE HOMOGENATES (1957)

For many years the van den Bergh react'ion has been utilized for the differentiation and quantitative measurement of t,he two forms of bilirubin found in the blood.One form, "direct" bilirubin, reacts instantaneously with diazotized sulfanilic acid.The second pigment, bilirubin or so called "indirect" bilirubin, reacts with the diazo reagent after the addition of alcohol (l), caffeine urea (2), or caffeine sodium benzoate (3).Despite the wide clinical use of the test for the differential diagnosis of jaundice, the chemical difference between these two pigments has not yet been established.Direct bilirubin has been postulated to be a protein complex (I), a heavy metal complex (4, 5), or an ester (6, 7) of bilirubin.Some authors have believed that only one pigment exists, the differences in reaction in the van den Bergh test being caused by substances in the serum (8-10).An excellent critical review of these interpretations has been made by With (11).Recently, Billing and.coworkers (12, 13) isolated and separated the two pigments on a kieselguhr column.The two compounds retained their specific diazo reactions despite the complete absence of all proteins.Similarly, Najjar and Childs ( 14) crystallized the two pigments and found that the protein-free crystals still possessed their original diazo reactions.Within the last few mont)hs Billing and Lathe (15) and Schmid ( 16) have isolated glucuronic: acid after t,he hydrolysis of "direct"' hilirubin azo pigment with alkali or p-glucuronidase.These aut)horx concluded that "direct" bilirubin is t,he product of the conjugation of bilirubin with glucuronic acid and is presumably formed in the liver.Dutton and Storey (17,18) have studied the synthesis in vitro of glucuronides of various phenols in liver homogenat,es.We have investigated the conversion of bilirubin to "direct" bilirubin in a similar system in order to demonstrate that glucuronide conjugation is the primary mechanism involved in the synthesis of "direct" bilirubin by the liver.EXPERIMESTAL Preparation oj Bilirubin Solution-A stock bilirubin solution was prepared by dissolving 10 mg. of bilirubin (Eastman 2101) in 100 ml. of chloro-
Purification and conformational properties of a human interferon α2b produced inEscherichia coli (2001)

Recombinant human interferon α2b was expressed intracellularly in Escherichia coli as insoluble aggregates using a new expression vector, and was purified to homogeneity using essentially two‐step chromatographic procedures, i.e. immobilized metal‐ion‐affinity chromatography and reversed‐phase HPLC. The established purification process is highly reproducible and leads to a total recovery of approx. 12% with a specific biological activity of higher than 1×10 8 i.u./mg of protein, which is comparable with the international requirement for interferon α2b. For purified protein we report conformational stability as a function of pH and temperature using differential scanning calorimetry and CD. Thermal unfolding as a function of pH showed only one endotherm at a temperature higher than 45 °C, and was reversible at pH 2–3.75 and irreversible at pH 4–10. At pH 7.0, the most stable condition, the conformational stability depends on protein concentration and ionic strength. The highly helical secondary structure is very conserved over the whole pH range studied, including at high temperatures.
2-Phenylindoles. Effect of N-benzylation on estrogen receptor affinity, estrogenic properties, and mammary tumor inhibiting activity (1987)

Hydroxy-2-phenylindoles carrying substituted benzyl groups and similar substituents at the nitrogen were synthesized and tested for their ability to displace estradiol from its receptor. All of the derivatives tested exhibited high binding affinities for the calf uterine estrogen receptor, with RBA values ranging from 0.55 to 16 (estradiol 100). The mouse uterine weight tested revealed only low estrogenicity for this class of compounds. Several derivatives showed antiestrogenic activity with a maximum inhibition of estrone-stimulated uterine growth of 40%. Two of the compounds (6c, 21c) were tested for antitumor activity in dimethylbenanthracene- (DMBA-) induced estrogen-dependent rat mammary tumors. Only the 4-cyanobenzyl derivative 21c was active. After 4 weeks of treatment with 12 mg/kg (6 times/week), the average tumor area was decreased by 57% (control +204%). In vitro, an inhibitory effect of 21b was only observed with hormone-sensitive MCF-7 breast cancer cells but not with hormone-independent MDA-MB 231 cells. These results make a mode of action involving the estrogen receptor system likely.
Reverberation chamber evaluation of multi-antenna handsets having low mutual coupling and high efficiencies (2006)

International audience
The Dip Test of Unimodality (1985)

The dip test measures multimodality in a sample by the maximum difference, over all sample points, between the empirical distribution function, and the unimodal distribution function that minimizes that maximum difference. The uniform distribution is the asymptotically least favorable unimodal distribution, and the distribution of the test statistic is determined asymptotically and empirically when sampling from the uniform.
Novel gain-transparent SOA-switch for high bitrate OTDM add/drop multiplexing (2002)

We demonstrate an all-optical switch with the inherent advantage of leaving the non-switched pulses undisturbed the switching principle is based on index modulations at 1.55 /spl mu/m that originate from gain saturation in a 1.3 /spl mu/m semiconductor optical amplifier.
Evolution of the serologic response to Borrelia burgdorferi in treated patients with culture-confirmed erythema migrans (1996)

We investigated the appearance and evolution of immunoglobulin M (IgM) and IgG antibodies to Borrelia burgdorferi in 46 patients with culture-proven erythema migrans (EM). All patients received antimicrobial treatment and were prospectively evaluated for up to 1 year. A total of 257 serially collected serum samples were tested by commercial IgG-IgM enzyme-linked immunosorbent assay and separate IgM and IgG immunoblots (IBs). At the baseline, 33% of the patients had a positive ELISA result and 43% of the patients had a positive IgM IB result by using the criteria of the Centers for Disease Control and Prevention-Association of State and Territorial Public Health Laboratory Directors for the interpretation of IB results. Positive serology at the baseline and the rate of seroconversion correlated directly with disease duration and/or evidence of dissemination prior to treatment. At days 8 to 14 after the baseline, 91% of patients had a positive ELISA result and/or IgM IB result. Peak IgM antibody levels were seen at this time in patients with localized or disseminated disease. The most frequent IgM bands at the baseline and the peak were of 24 kDa (OspC), 41 kDa, and 37 kDa. Although 89% of the patients developed IgG antibodies as determined at a follow-up examination, only 22% were positive by the IgG IB criteria of the Centers for Disease Control and Prevention-Association of State and Territorial Public Health Laboratory Directors. The persistence of antibodies was directly related to disease duration and/or dissemination prior to treatment. Since IgM antibodies to the 24- and 41-kDa antigens remained detectable for long periods, 38% of IgM IBs were still positive at 1 year postbaseline. IgM to antigens of 39, 58, 60, 66, or 93 kDa, conversely, were most often seen in sera obtained within 1 month postbaseline. Their presence may be of assistance in confirming a recent infection with B. burgdorferi in individuals living in areas where Lyme disease is endemic.