gebhart/patrepeval huggingface dataset:
Comparative ability of IL-12 and IL-28B to regulate Treg populations and enhance adaptive cellular immunity (2009)

Improving the potency of immune responses is paramount among issues concerning vaccines against deadly pathogens. IL-28B belongs to the newly described interferon lambda (IFNlambda) family of cytokines, and has not yet been assessed for its potential ability to influence adaptive immune responses or act as a vaccine adjuvant. We compared the ability of plasmid-encoded IL-28B to boost immune responses to a multiclade consensus HIV Gag plasmid during DNA vaccination with that of IL-12. We show here that IL-28B, like IL-12, is capable of robustly enhancing adaptive immunity. Moreover, we describe for the first time how IL-28B reduces regulatory T-cell populations during DNA vaccination, whereas IL-12 increases this cellular subset. We also show that IL-28B, unlike IL-12, is able to increase the percentage of splenic CD8(+) T cells in vaccinated animals, and that these cells are more granular and have higher antigen-specific cytolytic degranulation compared with cells taken from animals that received IL-12 as an adjuvant. Lastly, we report that IL-28B can induce 100% protection from mortality after a lethal influenza challenge. These data suggest that IL-28B is a strong candidate for further studies of vaccine or immunotherapy protocols.
Construction of random input-output codes with moderate block lengths (2014)

Random I/O (RIO) Codes, recently introduced by Sharon and Alrod, is a coding scheme to improve the random input/output performance of flash memories. Multi-level flash memories require, on the average, more than a single read threshold in order to read a single logical page. This number is important to be optimized since it sets the read latency of flash memories. An (n,M, t) RIO code assumes that t pages are stored in n cells with t + 1 levels. The first page is read by applying a read threshold between levels t and t + 1. Similarly, the second page is read by applying a read threshold between levels t - 1 and t, and so on. The read binary vectors for consecutive pages satisfy the property that the set of positions read with value 1 can only increase. Therefore, Sharon and Alrod showed also that the design of RIO codes is equivalent to the design of WOM codes. The latter family of codes attracted a lot of attention in recent years in order to improve the lifetime of flash memories by allowing to write multiple messages to the memory without the need for a physical erase. In this paper we notice two important distinctions between RIO codes and WOM codes. While in WOM codes the messages are received one after the other and thus are not known all in advance, in RIO codes the information of all logical pages can be known in advance when programming the cells. Even though this knowledge does not improve the capacity of RIO codes, it allows the design of efficient high-rate codes with a moderate block length, which are hard to be found for WOM codes. We also study another family of RIO codes, called here partial RIO Codes, that allow to find even more efficient codes in the tradeoff of reading more than a single threshold to read a page.
O’Donoghue Award Winner (2016)

Background: Altered knee kinematics after anterior cruciate ligament injury and reconstruction (ACLR) have been implicated in the development of premature osteoarthritis (OA), leading to poor long term clinical outcomes. Purpose: This study was performed to determine (1) whether average knee center of rotation (KCOR), a multidimensional metric of knee kinematics, of the ACLR knee during walking differs from that of the contralateral uninjured knee, (2) whether KCOR changes between 2 and 4 years after surgery, and (3) whether early KCOR changes predict patient reported outcomes 8 years after ACLR. Study Design: Prospective Clinical Study. Methods: Twenty-six human subjects underwent gait analysis with calculation of bilateral KCOR during walking at 2 and 4 years after unilateral ACLR. Knee injury and Osteoarthritis Outcome Scores (KOOS) and Lysholm scores were collected at 2, 4, and 8 years after ACLR in 13 of these subjects. Results: The ACLR knee showed greater medial compartment motion due to pivoting about a more lateral KCOR (P=0.03) than the uninjured contralateral knee at 2 years. KCOR moved medially over time (P=0.047), with values approaching those of the uninjured knee by 4 years (P=0.55). KCOR was also more anterior in the ACLR knee at 2 years (P=0.02). Between 2 and 4 years, KCOR moved posteriorly in 16 (62%) and anteriorly in 10 (38%) subjects. Increasing anterior position of KCOR in the ACLR knee from 2 to 4 years showed no correlation with clinical outcomes at 4 years but correlated with worsening clinical outcomes at 8 years: Lysholm (R2=0.41); KOOS pain (R2=0.37), symptoms (R2=0.58), and quality of life (R2=0.50). Conclusions: The observed changes to KCOR during walking between 2 and 4 years after ACLR show progressive improvement suggestive of continued graft maturation and neuromuscular recovery. The finding of increasingly abnormal kinematics correlating with reduced clinical outcomes years later in a subset of subjects provides a potential explanation for the incidence of premature OA following ACLR. These findings support progressing to more comprehensive studies of larger cohorts examining the predictive potential of KCOR for OA risk as measured by advanced quantitative imaging and radiographs. Clinical Relevance: These results suggest that changes to KCOR during walking as derived from gait analysis, a clinically available metric, may provide early warning of deteriorating knee function after ACLR years before the onset of clinical symptoms.
Link Bundling in MPLS Traffic Engineering (TE) (2005)

For the purpose of Generalized Multi-Protocol Label Switching (GMPLS) signaling, in certain cases a combination of <link identifier, label> is not sufficient to unambiguously identify the appropriate resource used by a Label Switched Path (LSP).Such cases are handled by using the link bundling construct, which is described in this document.This document updates the interface identification TLVs, which are defined in the GMPLS Signaling Functional Description.
Einleitung (1981)

Änderungen der horizontalen Windgeschwindigkeitskomponente mit der Höhe werden als Scherwinde bezeichnet. Sie entstehen durch Impulsaustausch in der bodennahen Grenzschicht und sind erfahrungsgemäß besonders intensiv beim Zusammentreffen von Kalt- und Warmluftfronten, in der Nähe von Gewittern oder an Inversionsschichten.
P1‐281: C‐terminal‐truncated apoE4 inefficiently clears amyloid‐beta peptides and synergizes with Abeta to elicit Alzheimer‐like deficits in mice (2010)

Apolipoprotein (apo) E4 is the major known genetic risk factor for late-onset familial and sporadic Alzheimer's disease (AD). However, the mechanistic role of apoE4 in the pathogenesis of AD is unclear. We previously showed that, as compared to apoE3, apoE4 preferentially undergoes aberrant cleavage in neurons, yielding C-terminal-truncated fragments. These apoE fragments, also identified in human brain lysates, impair both mitochondrial and cytoskeletal components in vitro and in vivo. Transgenic mice expressing high levels of C-terminal-truncated apoE4 in neurons [apoE4(Δ272-299)] had hippocampal neurodegeneration and behavioral deficits. Objective: To study the effect of the C-terminal-truncated apoE4 on beta-amyloid clearance/deposition and its potential synergistic role with beta-amyloid in eliciting AD-like deficits in mice. We cross-bred apoE4(Δ272-299) transgenic mice expressing low levels of apoE4 fragment with human APP-expressing mice harboring familial AD mutations (hAPPFAD, line J20) and tested the effects of the apoE4 fragment on beta-amyloid levels, deposition, and neuronal and behavioral deficits in mice at 5-9 months of age. Expression of apoE4(Δ272-299) reduced total hippocampal beta-amyloid levels by 63% and beta-amyloid deposition by 60% as compared to hAPPFAD mice without apoE. However, expression of the full-length apoE3 or apoE4 in hAPPFAD mice reduced beta-amyloid levels by 95% and 90%, respectively. Double immunostaining for apoE and beta-amyloid revealed that C-terminal-truncated apoE4 did not colocalize with beta-amyloid although the full-length apoE3 and apoE4 did. These results suggest that the C-terminal-truncated apoE4 does not bind well to beta-amyloid, leading to decreased clearance of beta-amyloid peptides from the brain and, thus, increased beta-amyloid deposition relative to full-length apoE. Interestingly, learning and other behavioral deficits in apoE4(Δ272-299)/hAPPFAD double transgenic mice remained similar to those in mice expressing hAPPFAD alone, despite the overall reductions in beta-amyloid levels and deposition in the double transgenic mice. In the elevated plus maze, mice expressing both apoE4(Δ272-299) and hAPPFAD had greater abnormal anxiety than mice expressing hAPPFAD alone. These results suggest that the C-terminal-truncated apoE4 fragments inefficiently clear beta-amyloid peptides, leading to increased beta-amyloid deposition, and synergize with beta-amyloid to elicit AD-like deficits in mice.
Environmental enrichment may alter the number of rats needed to achieve statistical significance (2019)

Currently, environmental enrichment studies have focused on detection of differences in group means resulting from varied enrichments. The effects of enrichment procedures on variation and hence on study results have received far less attention. Within group variation in studies is directly related to adequate sample size and thus determines ethically correct number of animals to be used. The aim of this study was to evaluate the effects of enrichment items on clinical chemistry and physiological parameters of Wistar rats with the emphasis on the extent of variation. Fortyeight weaned female and male outbred Wistar rats from eight different litters were housed for five weeks in groups of four rats per cage with an aspen tube (20x12x12 em), an aspen block (6x6x6 cm) or without enrichment items (control animals). At the end of the study, adrenals and brown adipose tissues were weighed, growth calculated from initial and final body weights and the following assays were performed from serum samples: AFOS, ALAT, ASAT, LDH, GGT, Pi, Ca, cholesterol, triglycerides, ereatinine, total bilirubin, protein and corticosterone. Based on the variation detected, SOLO Power Analysis was used to calculate the smallest number of animals required (n) to detect an arbitrarily chosen 20 % difference in all means, when significance was set at p=0.05 and statistical power at 0.90. Based on the n-values, additional N-ratio (nenrichment / ncontrol) was calculated to indicate, how many times more or less animals were needed in the enrichment group in comparison to the control group. The enrichment items did not have effects on group means. However. they seemed to influence the variation and hence on the number of animals needed, with enzyme parameters being the most sensitive in this respect. This relationship between enrichment, variation and number of animals needed should be kept in mind while designing experiments with ethically correct sample size.
Percutaneous Transhepatic Venous Sampling of Gastrin (1982)

REPORTS of the preoperative localization of gastrinomas by percutaneous transhepatic venous sampling1 , 2 have been published, but the data are scanty. Successful identification of a solitary and sporadic nonfamilial gastrinoma may dictate surgical excision of the tumor rather than total gastrectomy.2 , 3 On the other hand, G-cell hyperfunction, a rare cause of hypergastrinemia and florid peptic-ulcer disease, may be confused with gastrinoma but responds to simple antrectomy and vagotomy. The value of transhepatic venous sampling in multiple endocrine neoplasia type I, in which multiple adenomatosis or tumors may occur, has not been evaluated.To assess the value of transhepatic venous sampling, we . . .
ChemInform Abstract: Rapid Wolff—Kishner Reductions in a Silicon Carbide Microreactor. (2014)

Abstract The reaction is performed in a novel silicon carbide microreactor.
Message passing over windows-based desktop grids (2006)

Message Passing is a popular mechanism used to enable inter-process communication in parallel and distributed computing. Many complex scientific and engineering applications that are executed on clusters have been developed based on this communication model. Due to the huge amount of computing power being wasted in desktops, there is an increasing interest in using these computers to execute complex applications. However, most of the current middleware systems are aimed at executing only embarrassingly parallel applications, i.e. with no inter-process communication. Moreover, most existing middleware systems are based on Linux. Nevertheless, it is well-known that the desktop machines in the world are predominantly based on the Windows operating system. Hence, in this work we present the design implementation and evaluation performance of a Windows-based implementation of two message passing models, Message Passing Interface (MPI) and Bulk Synchronous Parallel (BSP), over the Alchemi Grid computing framework.
A Probability Neural Network (PNN) Estimator for Improved Reliability of "Noisy" Sensor Data (1991)

A self-directed, real-time, material processing system known as Qualita tive Process Automation (QPA) employs a knowledge base for autoclave curing of compos ites which requires information related to the "velocity" (d/dt) and "acceleration" (d 2 /dt 2 ) of temperature during the process of curing. The problem with using such information is the susceptibility of sensed data to process noise which results in sporadic, inconsistent and thus unreliable process data. To improve the reliability of "noisy" sensor data and therein the performance of a self-directed, real-time material processing system, an esti mator based on a Probability Neural Net (PNN) was developed. The paper is organized to: first, address the pertinent and distinguishing properties of PNNs, as well as reasons for their use in the QPA autoclave curing application, second, to suggest a methodology for coping with the practical difficulties of PNNs, and finally, to present the computational results of this study. A conclusion section focuses on the identification of other PNN appli cations, and some future PNN research.
Transcutaneous Intraluminal Impedance Measurement for Minimally Invasive Monitoring of Gastric Motility: Validation in Acute Canine Models (2014)

Transcutaneous intraluminal impedance measurement (TIIM) is a new method to cutaneously measure gastric contractions by assessing the attenuation dynamics of a small oscillating voltage emitted by a battery-powered ingestible capsule retained in the stomach. In the present study, we investigated whether TIIM can reliably assess gastric motility in acute canine models. Methods. Eight mongrel dogs were randomly divided into 2 groups: half received an active TIIM pill and half received an identically sized sham capsule. After 24-hour fasting and transoral administration of the pill (active or sham), two force transducers (FT) were sutured onto the antral serosa at laparotomy. After closure, three standard cutaneous electrodes were placed on the abdomen, registering the transluminally emitted voltage. Thirty-minute baseline recordings were followed by pharmacological induction of gastric contractions using neostigmine IV and another 30-minute recording. Normalized one-minute baseline and post-neostigmine gastric motility indices (GMIs) were calculated and Pearson correlation coefficients (PCCs) between cutaneous and FT GMIs were obtained. Statistically significant GMI PCCs were seen in both baseline and post-neostigmine states. There were no significant GMI PCCs in the sham capsule test. Further chronic animal studies of this novel long-term gastric motility measurement technique are needed before testing it on humans.
Design progress for the National Ignition Facility laser alignment and beam diagnostics (1999)

Earlier papers have described approaches to NIF alignment and laser diagnostics tasks. Now, detailed design of alignment and diagnostic systems for the National Ignition Facility (NIF) laser is in its last year. Specifications are more detailed, additional analyses have been completed, Pro- E models have been developed, and prototypes of specific items have been built. In this paper we update top level concepts, illustrate specific areas of progress, and show design implementations as represented by prototype hardware. The alignment light source network has been fully defined. It utilizes an optimized number of lasers combined with fiber optic distribution to provide the chain alignment beams, system centering references, final spatial filter pinhole references, target alignment beams, and wavefront reference beams. The input and output sensor are being prototyped. They are located respectively in the front end just before beam injection into the full aperture chain and at the transport spatial filter, where the full energy infrared beam leaves the laser. The modularity of the input sensor is improved, and each output sensor mechanical package now incorporates instrumentation for four beams.
Pharmacologic Prophylaxis of Calcium Stones (2007)

The management of nephrolithiasis forms an important part of urologic practice. The recurrence rate after forming an initial stone is reported to be as high as 50% at 5 yr and 80–90% at 10 yr, highlighting the importance of medical prophylactic therapy. A better understanding of pathophysiology and formulation of diagnostic criteria for different etiologies of nephrolithiathis have made feasible the adoption of selective treatment programs. the objectives of medical stone management should be: 1. Correct the Underlying Phisiocochemical and Phisiologic derannagements. 2. Prevent new stone formation. 3. Avoid nonrenalcomplicatations of the disease Process. 4. Be free of serious side-effects. Key WordsNephrolithiasismedical managementprophylaxiscalciumdiuretic
Radical Exchange Reactions between Vitamin E, Vitamin C and Phospholipids in Autoxidizing Polyunsaturated Lipids (1994)

Antioxidant reactions of mixtures of vitamin E, vitamin C and phospholipids in autoxidizing lipids at 90 degrees C have been studied by ESR spectroscopy. When the phospholipid contained a tertiary amine (e.g. phosphatidylcholine), the vitamin C and the vitamin E radicals were successively observed as these two vitamins were sequentially oxidised during lipid oxidation. In the presence of the primary amine contained in phosphatidylserine, the vitamin E oxidation was delayed for a few hours. In this case neither the vitamin C, nor the vitamin E radicals but a nitroxide radical derived from the phospholipid was observed. Similar results to those obtained with PS were obtained in the presence of either phosphatidylethanolamine or soybean lecithin. The participation in the radical reactions of phospholipids possessing a primary amine can therefore explain the synergistic effect of these phospholipids in a mixture of vitamins E and C.
The design and synthesis of a novel series of androgen receptor antagonists leading to the discovery of the clinical candidate BMS-641988 (2008)

1314 Carcinoma of the prostate (CaP) is the 2 nd leading cause of cancer-related death in men in the United States. Androgen ablation via surgical or chemical castration or by treatment with an antiandrogen is currently the treatment of choice for advanced CaP. Although this therapy initially shows an 80-90% response rate, approximately 50% of patients progress to fatal androgen independent CaP (AI-CaP) after about 18 months of treatment. Recent advances in the field have shown that reactivation of the androgen receptor (AR) signaling pathway is the root cause for the development of AI-CaP. The identification of the role of the AR in AI-CaP suggests that new agents that act at the level of the AR may be effective in the treatment of this disease. Here will be presented structure-based design efforts to identify novel chemotypes that show potent binding to, and antagonism of, the AR. In particular, a series of [2.2.1]-oxobicyclic imide-based AR antagonists showed great promise and the structure activity relationships (SAR) of this novel series will be presented in detail. All new analogs were screened via whole cell competitive binding and transactivation assays in MB-MDA-453 cells to generate in vitro SAR around the wild-type AR. Promising leads from these in vitro assays were then screened through an immature rat prostate weight PK/PD model (IRPW, PO, QD x 4 days). Analogs showing optimal PK and PD effects in the IRPW were then tested in the human cancer xenograft model CWR22, implanted in nude mice. These approaches resulted in the identification of BMS-641988 as a development candidate for the treatment of advanced CaP.
Free Access Distributed Queue Protocol for Massive Cellular-Based M2M Communications with Bursty Traffic (2018)

Long Term Evolution (LTE) networks are expected to play a key role in providing connections to billions of Machine-Type Devices (MTDs) in the 5G big picture. Since the ALOHA-based access framework of LTE-A alone cannot support bursty massive access scenarios caused by the MTDs, the 3GPP has additionally employed the Access Class Barring (ACB) scheme as the baseline traffic control method. While the scheme certainly improves access success probability of the devices, corresponding delay degradation may be unacceptable. In this paper, we renounce the ALOHA-based framework of LTE to propose a new protocol, namely the Free Access Distributed Queue (FADQ), accompanied by an estimation method to resolve the massive synchronized access issue in a more efficient manner. Simulations under the 3GPP's reference setup show that FADQ protocol significantly reduces access delay while maintaining an access success probability on par with the ACB.
Polycomb CBX7 Promotes Initiation of Heritable Repression of Genes Frequently Silenced with Cancer-Specific DNA Hypermethylation (2009)

Epigenetic silencing of genes in association with aberrant promoter DNA hypermethylation has emerged as a significant mechanism in the development of human cancers. Such genes are also often targets of the polycomb group repressive complexes in embryonic cells. The polycomb repressive complex 2 (PRC2) has been best studied in this regard. We now examine a link between PRC1 and cancer-specific gene silencing. Here, we show a novel and direct association between a constituent of the PRC1 complex, CBX7, with gene repression and promoter DNA hypermethylation of genes frequently silenced in cancer. CBX7 is able to complex with DNA methyltransferase (DNMT) enzymes, leading us to explore a role for CBX7 in maintenance and initiation of gene silencing. Knockdown of CBX7 was unable to relieve suppression of deeply silenced genes in cancer cells; however, in embryonal carcinoma (EC) cells, CBX7 can initiate stable repression of genes that are frequently silenced in adult cancers. Furthermore, we are able to observe assembly of DNMTs at CBX7 target gene promoters. Sustained expression of CBX7 in EC cells confers a growth advantage and resistance to retinoic acid-induced differentiation. In this setting, especially, there is increased promoter DNA hypermethylation for many genes by analysis of specific genes, as well as through epigenomic studies. Our results allow us to propose a potential mechanism through assembly of novel repressive complexes, by which the polycomb component of PRC1 can promote the initiation of epigenetic changes involving abnormal DNA hypermethylation of genes frequently silenced in adult cancers.