gebhart/patrepeval huggingface dataset:
2-Aminoadipate-2-Oxoglutarate Aminotransferase Isoenzymes in Human Liver: A Plausible Physiological Role in Lysine and Tryptophan Metabolism (1993)

Two major 2-aminoadipate aminotransferase (AadAT) activities of human liver extract were separated by DEAE-Sepharose column chromatography. The faster eluting enzyme was designated AadAT-I and the other one AadAT-II. AadAT-I had a hgih Km value for aminoadipate, 20 mmol/l, and a low Km value for glutamate, 1.4 mmol/l. In contrast, AadAT-II had a low Km value for aminoadipate, 0.25 mmol/l, and a high Km value for glutamate, 12.5 mmol/l. AadAT-I and AadAT-II were mainly localized in the supernatant and mitochondrial fraction, respectively. AadAT-I demonstrated only glutamate-2-oxoadipate or 2-aminoadipate-2-oxoglutarate aminotransferase activities. AadAT-II further showed the activity of tryptophan and kynurenine. On the basis of Km values and subcellular localization of the isoenzymes, a plausible role was suggested for them involving the metabolism of lysine and tryptophan.
Urine Detection of Survivin is a Sensitive Marker for the Noninvasive Diagnosis of Bladder Cancer (2004)

Urine survivin was a strong, independent predictor of the presence of bladder cancer and higher tumor grade. Urine detection of survivin is an accurate diagnostic test for bladder cancer that retains its efficiency regardless of cancer stage and grade.
Temporal and lineage-specific control of T cell receptor alpha/delta gene rearrangement by T cell receptor alpha and delta enhancers. (1994)

To analyze the regulation of gene rearrangement at the T cell receptor (TCR) alpha/delta locus during T cell development, we generated transgenic mice carrying a human TCR delta gene minilocus. We previously showed that the presence of the TCR delta enhancer (E delta) within the J delta 3-C delta intron was required to activate a specific step (V-D to J) of transgene rearrangement, and that rearrangement was activated equivalently in the precursors of alpha beta and gamma delta T cells. To further explore the role of transcriptional enhancers in establishing the developmental pattern of gene rearrangement at the TCR alpha/delta locus, we substituted the TCR alpha enhancer (E alpha) in place of E delta within the transgenic minilocus. We found that V-D-J rearrangement of the E alpha+ minilocus was restricted to the alpha beta T cell subset. Further, we found that although V-D-J rearrangement of the E delta+ minilocus was initiated in the fetal thymus by day 14.5, V-D-J rearrangement of the E alpha+ minilocus did not occur until fetal day 16.5. Finally, whereas V-D-J rearrangement of the E delta+ minilocus is essentially completed within the triple negative population of postnatal thymocytes, V-D-J rearrangement of the E alpha+ minilocus is only initiated late within this population. Since the properties of minilocus rearrangement under the control of E delta and E alpha parallel the properties of V delta-D delta-J delta and V alpha-J alpha rearrangement at the endogenous TCR alpha/delta locus, we conclude that these enhancers play an important role in orchestrating the developmental program of rearrangements at this locus.
IP Encapsulating Security Payload (ESP) (1995)

IP Encapsulating
A multicenter study of recombinant factor VIII (recombinate): safety, efficacy, and inhibitor risk in previously untreated patients with hemophilia A. The Recombinate Study Group. (1994)

In July 1990, the Recombinate Study Group initiated a prospective, open-labeled investigation of recombinant factor VIII (r-FVIII) to assess its safety and efficacy and to characterize the natural history of inhibitor development in previously untreated patients (PUPs) with hemophilia A. All study subjects have severe FVIII deficiency (baseline FVIII level < or = 2% of normal) and no history of blood product exposure before study entry. Following the first r-FVIII infusion, plasma was screened for inhibitors once every 3 months, and plasma recovery of r-FVIII at 30 minutes and 24 hours postinfusion was assayed at least once every 6 months. As of May 1993, 73 of 79 patients originally enrolled in the trial continue to participate. The median number of r-FVIII exposure-days for the 71 subjects who have received at least one r-FVIII infusion is 11. A total of 1,785 infusions have been administered to treat 810 bleeding events. Ninety-two percent of bleeding events responded as anticipated to one or two infusions. Two, nonrecurring, acute adverse reactions occurred coincident with r-FVIII infusion, one of which was unrelated and the other, possibly related to the infusion. Seventeen (23.9%) subjects have developed inhibitors: five with peak titers more than 10 Bethesda units (BU) and 12 with peak titers < or = 10 BU (range, 0.5 to 10). Survival analysis showed that the probability of remaining inhibitor-free in this group of patients with severe hemophilia A is 88.4% after 8, 73.6% after 10, and 61.6% after 25 r-FVIII exposure-days. Inhibitors disappeared in five (29.4%) subjects on retesting 2 to 16 months after the last positive inhibitor assay. r-FVIII is safe and effective in the treatment of hemophilia A-related bleeding. To date, the inhibitor risk associated with its use is comparable to that in patients treated with plasma-derived concentrates. The majority of inhibitors identified are low in titer and do not preclude continued on-demand therapy with r-FVIII.
New advances in prevention of migraine (2016)

Despite being one of the most common disabling primary headaches, migraine continues to be underdiagnosed and under-treated. A migraine challenges not only the patient suffering from the migraine, but also physicians; especially in recognizing candidates for prophylaxis and selecting the appropriate preventive medication. Recently, there have been major advances in the diagnosis and treatment of migraine, with different guidelines of migraine management across the world. Here, we review migraines abortive and prophylactic medications, based on their pharmacologic category, citing their recommended doses, efficacy, and side effects. Additionally, we highlight the prophylactic treatment of specific patient populations and present suggested treatment approaches in view of recent international treatment guidelines that consider factors other than drug efficacy when choosing the optimal preventive therapy. Finally, we introduce drugs in different stages of development, which have novel mechanisms of action or have new therapeutic targets.
Serial Analysis of Gene Expression (1995)

The characteristics of an organism are determined by the genes expressed within it. A method was developed, called serial analysis of gene expression (SAGE), that allows the quantitative and simultaneous analysis of a large number of transcripts. To demonstrate this strategy, short diagnostic sequence tags were isolated from pancreas, concatenated, and cloned. Manual sequencing of 1000 tags revealed a gene expression pattern characteristic of pancreatic function. New pancreatic transcripts corresponding to novel tags were identified. SAGE should provide a broadly applicable means for the quantitative cataloging and comparison of expressed genes in a variety of normal, developmental, and disease states.
Electronic medical record-based multicondition models to predict the risk of 30 day readmission or death among adult medicine patients: validation and comparison to existing models (2015)

A new electronic multicondition model based on information derived from the EMR predicted mortality and readmission at 30 days, and was superior to previously published claims-based models.
VRSync: Characterizing and eliminating synchronization-induced voltage emergencies in many-core processors (2012)

Power consumption is a primary concern for microprocessor designers. Lowering the supply voltage of processors is one of the most effective techniques for improving their energy efficiency. Unfortunately, low-voltage operation faces multiple challenges going forward. One such challenge is increased sensitivity to voltage fluctuations, which can trigger so-called “voltage emergencies” that can lead to errors. These fluctuations are caused by abrupt changes in power demand, triggered by processor activity variation as a function of workload. This paper examines the effects of voltage fluctuations on future many-core processors. With the increase in the number of cores in a chip, the effects of chip-wide activity fluctuation - such as that caused by global synchronization in multithreaded applications - overshadow the effects of core-level workload variability. Starting from this observation, we developed VRSync, a novel synchronization methodology that uses emergency-aware scheduling policies that reduce the slope of load fluctuations, eliminating emergencies. We show that VRSync is very effective at eliminating emergencies, allowing voltage guardbands to be significantly lowered, which reduces energy consumption by an average of 33%.
Fibroblasts from Ataxia Telangiectasia (AT) and AT Heterozygotes Show an Enhanced Level of Residual DNA Double-strand Breaks after Low Dose-rate γ-irradiation as Assayed by Pulsed Field Gel Electrophoresis (1991)

Skin fibroblasts from ataxia telangiectasia (AT) patients, obligate AT heterozygotes (ATH) and normal individuals were studied for colony-forming ability and repair of DNA double-strand breaks (dsb) after gamma-irradiation. AT cells were three to four times more radiosensitive than normal cells at high and low dose-rate exposures; ATH cells, however, showed a marginally increased radiosensitivity after high dose-rate gamma-irradiation and an intermediate response after low dose-rate exposure. The repair of DNA dsb was studied by pulsed field gel electrophoresis. After high dose-rate gamma-irradiation the repair time constant (t1/2) was around 1 h for normal, ATH and AT cells. After low dose-rate gamma-irradiation the fraction of residual dsb was 1.4% for normal, 2.1% for ATH and 5.2% for AT cells, demonstrating a deficiency in the repair of a small fraction of dsb in AT. Thus the fraction of residual dsb after low dose-rate exposure was not only four times higher in AT than in normal cells, but was also significantly increased in ATH compared to normal cells.
Extensive CDR3H Length Heterogeneity Exists in Bovine Foetal VDJ Rearrangements (2002)

Analysis of seven variable-diversity-joining (VDJ) gene rearrangements in B splenocytes from a 125-day-old bovine foetus revealed an extensive heavy-chain complementarity-determining region 3 (CDR3H) length variation (9-56 codons). Indeed, the global CDR3H size spectratyping of foetal VDJ rearrangements substantiated such an extensive heterogeneity and was comparable with that noted in peripheral B lymphocytes of adult cattle. These observations are in contrast to species such as humans with extensive germline combinatorial capability where shorter CDR3H length is noted early during B-cell development. Exceptionally long CDR3H (as in adult cattle) was noted in two foetal VDJ rearrangements encoded by a single germline VH gene. Further, two VH genes (gl.110.20 and BF2B5) were preferentially expressed in the foetal VDJ rearrangements. The DH gene-encoded CDR3H region of foetal VDJ rearrangements is remarkable for repetitive GGT (glycine) and TAT (tyrosine) codons that favour the recruitment of somatic hypermutations. It appears that closely related germline DH genes, preferentially used in the hydrophilic reading frame, encode varying CDR3H lengths early during B-cell ontogeny in cattle. A comparison of germline and expressed VH genes, especially in the CDR1 and CDR2, confirms that somatic hypermutations contribute to immunoglobulin (Ig)M antibody diversification in cattle. The biased nucleotide base use and high occurrence of 'hot-spot' triplet (AGPy; AG pyrimidine base) in the CDRs predisposes to somatic hypermutations. Overall, these observations suggest that extensive CDR3H length heterogeneity, including the generation of exceptionally long CDR3H (up to 56 amino acids), and somatic hypermutations contribute to IgM antibody diversification in cattle. The extensive CDR3H length heterogeneity early during the B-cell development may compensate for constraints imposed on antibody diversification owing to the limited germline sequence diversity of genetic elements in cattle.
TurboReg and Other ImageJ Plugins at the Biomedical Imaging Group of EPFL (2012)

We briefly present a non-exhaustive digest of some of the ImageJ plugins that were developed through the years by many authors at the Biomedical Imaging Group. While these plugins rely on advanced mathematical and algorithmic tools, we believe their user interface to be friendly enough that even non-experts can feel comfortable using them. We then focus on the specific plugin named TurboReg, which has been well received by many users. We look at it from a historical perspective, from its inception to its current state, discussing issues like development, coding, testing, deployment, documentation, update, extension, and user support. We draw a few lessons gained during its life cycle Biography Philippe Thevenaz was born in 1962 in Lausanne, Switzerland. He graduated in 1986 from the Ecole polytechnique federale de Lausanne (EPFL), Switzerland, with a diploma in microengineering. He joined the Institute of Microtechnology (IMT) of the University of Neuchâtel, Switzerland, where he obtained his Ph.D. in 1993. He then worked as a Visiting Fellow with the Biomedical Engineering and Instrumentation Program, National Institutes of Health (NIH), Bethesda MD, USA, where he developed research interests that include splines and multiresolution signal representations, geometric image transformations, and biomedical image registration. Since 1998, he is with the EPFL as senior researcher.
Two Classes of Highly Similar Coiled Coil-Nucleotide Binding-Leucine Rich Repeat Genes Isolated from the Rps1-k Locus Encode Phytophthora Resistance in Soybean (2005)

A series of single genes protect soybean from the root and stem disease caused by the oomycete pathogen Phytophthora sojae. In the last two decades, Rps1-k has been the most stable and widely used Phytophthora resistance gene for the major soybean-producing regions of the United States. Four highly similar genes encoding coiled coil-nucleotide binding-leucine rich repeat (CC-NB-LRR)-type proteins were isolated from the Rps1-k locus. These genes were grouped into two classes based on their sequence identity. Class I contains three genes with identical open reading frames (ORF) and 5' end regions. Two of these genes were also identical at the 3' untranslated regions; the third gene showed a recombination breakpoint in the 3' untranslated region resulting in the combination of 3' end sequences of members from both classes. Reverse transcription-polymerase chain reaction analyses suggested that members of both classes of genes are transcribed at low levels. Representative members from each gene class were expressed in transgenic soybean plants. Analyses of independent R0, R1, R2, and R3 progeny populations suggested that both gene classes confer Phytophthora resistance in soybean. A possible evolutionary mechanism for the Class I gene family is proposed.
Memory and complexity reduction in parahermitian matrix manipulations of PEVD algorithms (2016)

A number of algorithms for the iterative calculation of a polynomial matrix eigenvalue decomposition (PEVD) have been introduced. The PEVD is a generalisation of the ordinary EVD and will diagonalise a parahermitian matrix via paraunitary operations. This paper addresses savings - both computationally and in terms of memory use - that exploit the parahermitian structure of the matrix being decomposed, and also suggests an implicit trimming approach to efficiently curb the polynomial order growth usually observed during iterations of the PEVD algorithms. We demonstrate that with the proposed techniques, both storage and computations can be significantly reduced, impacting on a number of broadband multichannel problems.
Transporting real-time video over the Internet: challenges and approaches (2000)

Delivering real-time video over the Internet is an important component of many Internet multimedia applications. Transmission of real-time video has bandwidth, delay, and loss requirements. However the current Internet does not offer any quality of service (QoS) guarantees to video transmission over the Internet. In addition, the heterogeneity of the networks and end systems makes it difficult to multicast Internet video in an efficient and flexible way. Thus, designing protocols and mechanisms for Internet video transmission poses many challenges. In this paper, we take a holistic approach to these challenges and present solutions from both transport and compression perspectives. With the holistic approach, we design a framework for transporting real-time Internet video, which includes two components, namely, congestion control and error control. Specifically congestion control consists of rate control, rate-adaptive encoding, and rate shaping; error control consists of forward error correction (FEC), retransmission error resilience, and error concealment. For the design of each component in the framework, we classify approaches and summarize representative research work. We point out there exists a design space which can be explored by video application designers and suggest that the synergy of both transport and compression could provide good solutions.
BepiPred-2.0: improving sequence-based B-cell epitope prediction using conformational epitopes (2017)

Antibodies have become an indispensable tool for many biotechnological and clinical applications. They bind their molecular target (antigen) by recognizing a portion of its structure (epitope) in a highly specific manner. The ability to predict epitopes from antigen sequences alone is a complex task. Despite substantial effort, limited advancement has been achieved over the last decade in the accuracy of epitope prediction methods, especially for those that rely on the sequence of the antigen only. Here, we present BepiPred-2.0 (http://www.cbs.dtu.dk/services/BepiPred/), a web server for predicting B-cell epitopes from antigen sequences. BepiPred-2.0 is based on a random forest algorithm trained on epitopes annotated from antibody-antigen protein structures. This new method was found to outperform other available tools for sequence-based epitope prediction both on epitope data derived from solved 3D structures, and on a large collection of linear epitopes downloaded from the IEDB database. The method displays results in a user-friendly and informative way, both for computer-savvy and non-expert users. We believe that BepiPred-2.0 will be a valuable tool for the bioinformatics and immunology community.
Successful Treatment of Cushing’s Syndrome with the Glucocorticoid Antagonist RU 486* (1985)

A patient with Cushing's syndrome due to ectopic ACTH secretion was treated successfully with the new glucocorticoid antagonist RU 486 [17 beta-hydroxy-11 beta-(4-dimethylamino phenyl) 17 alpha-(1-propynyl)estra-4,9-dien-3-one]. This compound is a 19-nor steroid with substitutions at positions C11 and C17 which antagonizes cortisol action competitively at the receptor level. Oral RU 486 was given in increasing doses of 5, 10, 15, and 20 mg/kg . day for a 9-week period. Treatment efficacy was monitored by assessment of clinical status and by measuring several glucocorticoid-sensitive variables, including fasting blood sugar, blood sugar 120 min after oral glucose administration, and plasma concentrations of TSH, corticosteroid-binding globulin, LH, testosterone-estradiol-binding globulin, and total and free testosterone. With therapy, the somatic features of Cushing's syndrome (buffalo hump, central obesity, and moon facies) ameliorated, mean arterial blood pressure normalized, suicidal depression resolved, and libido returned. All biochemical glucocorticoid-sensitive parameters normalized. No side-effects of drug toxicity were observed. We conclude that RU 486 may provide a safe, well tolerated, and effective medical treatment for hypercortisolism.
A Molecularly Imprinted Electrochemical Gas Sensor to Sense Butylated Hydroxytoluene in Air (2018)

Alzheimer’s disease (AD) is a neurodegenerative disease, which affects millions of people worldwide. Curing this disease has not gained much success so far. Exhaled breath gas analysis offers an inexpensive, noninvasive, and immediate method for detecting a large number of diseases, including AD. In this paper, a new method is proposed to detect butylated hydroxytoluene (BHT) in the air, which is one of the chemicals found in the breath print of AD patients. A three-layer sensor was formed through deposition of a thin layer of graphene onto a glassy carbon substrate. Selective binding of the analyte was facilitated by electrochemically initiated polymerization of a solution containing the desired target molecule. Subsequent polymerization and removal of the analyte yielded a layer of polypyrrole, a conductive polymer, on top of the sensor containing molecularly imprinted cavities selective for the target molecule. Two sets of sensors have been developed. First, the graphene sensor has been fabricated with a layer of reduced graphene oxide (RGO) and tested over 5–100 part per million (ppm). For the second batch, Prussian blue was added to graphene before polymerization, mainly for enhancing the electrochemical properties. The sensor was tested over 0.02-1 parts per billion (ppb) level of concentration while the sensor resistance has been monitored.
Effect of Onconase on double-stranded RNA in vitro. (2009)

Onconase is a cytotoxic ribonuclease which targets tumor cells in vivo and in vitro. To date, cellular tRNA appeared to be the major target for Onconase mediated cytotoxic activity. Most recently we demonstrated that Onconase can also cleave double-stranded RNA (dsRNA). Incubation of Onconase at 37 degrees C with GAPDH gene-dsRNA (approximately 440 bp long) and dsRNA ladder showed degradation of dsRNA into a spectrum of smaller dsRNA fragments. Moreover, incubation of dsRNA substrates at 40 degrees C under similar conditions markedly potentiated further cleavage of dsRNAs. The recently discovered double-stranded RNase activity of Onconase suggests another mechanism for inducing cell death/apoptosis in malignant phenotypes via the RNA interference mechanism involving siRNA and miRNA.
Sirtuins in mammals: insights into their biological function (2007)

Sirtuins are a conserved family of proteins found in all domains of life. The first known sirtuin, Sir2 (silent information regulator 2) of Saccharomyces cerevisiae, from which the family derives its name, regulates ribosomal DNA recombination, gene silencing, DNA repair, chromosomal stability and longevity. Sir2 homologues also modulate lifespan in worms and flies, and may underlie the beneficial effects of caloric restriction, the only regimen that slows aging and extends lifespan of most classes of organism, including mammals. Sirtuins have gained considerable attention for their impact on mammalian physiology, since they may provide novel targets for treating diseases associated with aging and perhaps extend human lifespan. In this review we describe our current understanding of the biological function of the seven mammalian sirtuins, SIRT1-7, and we will also discuss their potential as mediators of caloric restriction and as pharmacological targets to delay and treat human age-related diseases.