gebhart/patrepeval huggingface dataset:
CXCR4 up-regulation by imatinib induces chronic myelogenous leukemia (CML) cell migration to bone marrow stroma and promotes survival of quiescent CML cells (2008)

Abstract Chronic myelogenous leukemia (CML) is driven by constitutively activated Bcr-Abl tyrosine kinase, which causes the defective adhesion of CML cells to bone marrow stroma. The overexpression of p210Bcr-Abl was reported to down-regulate CXCR4 expression, and this is associated with the cell migration defects in CML. We proposed that tyrosine kinase inhibitors, imatinib or INNO-406, may restore CXCR4 expression and cause the migration of CML cells to bone marrow microenvironment niches, which in turn results in acquisition of stroma-mediated chemoresistance of CML progenitor cells. In KBM5 and K562 cells, imatinib, INNO-406, or IFN-α increased CXCR4 expression and migration. This increase in CXCR4 levels on CML progenitor cells was likewise found in samples from CML patients treated with imatinib or IFN-α. Imatinib induced G0-G1 cell cycle block in CML cells, which was further enhanced in a mesenchymal stem cell (MSC) coculture system. MSC coculture protected KBM-5 cells from imatinib-induced cell death. These antiapoptotic effects were abrogated by the CXCR4 antagonist AMD3465 or by inhibitor of integrin-linked kinase QLT0267. Altogether, these findings suggest that the up-regulation of CXCR4 by imatinib promotes migration of CML cells to bone marrow stroma, causing the G0-G1 cell cycle arrest and hence ensuring the survival of quiescent CML progenitor cells. [Mol Cancer Ther 2008;7(1):48–58]
THE RESPIRATION AND CYTOCHROME OXIDASE ACTIVITY OF RAT AORTA IN EXPERIMENTAL HYPERTENSION (1959)

Oxygen consumption and cytochrome oxidase activity of aortas of rats with experimental hypertension were found to be higher than the corresponding values for aortas of normotensive animals. The higher metabolic activity of aortas of hypertensive animals appeared to be due both to an increase in the proportion of muscle cells to connective tissue fibers and to a higher activity of the intracellular portion of the tissue.
Robust Multichannel Blind Deconvolution via Fast Alternating Minimization (2011)

Blind deconvolution, which comprises simultaneous blur and image estimations, is a strongly ill-posed problem. It is by now well known that if multiple images of the same scene are acquired, this multichannel (MC) blind deconvolution problem is better posed and allows blur estimation directly from the degraded images. We improve the MC idea by adding robustness to noise and stability in the case of large blurs or if the blur size is vastly overestimated. We formulate blind deconvolution as an l(1) -regularized optimization problem and seek a solution by alternately optimizing with respect to the image and with respect to blurs. Each optimization step is converted to a constrained problem by variable splitting and then is addressed with an augmented Lagrangian method, which permits simple and fast implementation in the Fourier domain. The rapid convergence of the proposed method is illustrated on synthetically blurred data. Applicability is also demonstrated on the deconvolution of real photos taken by a digital camera.
LIPID-BASED FORMULATIONS FOR ORAL ADMINISTRATION: OPPORTUNITIES FOR BIOAVAILABILITY ENHANCEMENT AND LIPOPROTEIN TARGETING OF LIPOPHILIC DRUGS (2001)

The identification of increasingly complex intracellular drug targets, escalating requirements in terms of drug potency and the use of combinatorial chemistry libraries and in vitro receptor-based ...
Preserving location privacy in wireless lans (2007)

The broadcast and tetherless nature of wireless networks and the widespread deployment of Wi-Fi hotspots makes it easy to remotely locate a user by observing her wireless signals. Location is private information and can be used by malicious individuals for blackmail, stalking, and other privacy violations. In this paper, we analyze the problem of location privacy in wireless networks and present a protocol for improving location privacy. Our basic approach is to obfuscate several types of privacy-compromising information revealed by a mobile node, including sender identity, time of transmission, and signal strength. Our design is driven by real-system implementation and field experiments along with analysis and simulations. Our system allows users to choose the level of privacy they desire, thereby increasing the performance of less private users (while not sacrificing private users' privacy at the same time). We evaluated our system based on real-life mobility data and wireless LAN coverage. Our results show that a user of our system can be indistinguishable from a thousand users in the same coverage area.
Present and future trends of laser materials processing in Japan (1991)

Lasers quickly penetrated into Japanese industries in the mid-80s. The paper reviews the present situation of industrial lasers and their applications in Japanese industries for materials removal, joining, and some surface modification technologies as well as their economical evaluation compared with competitive technologies. Laser cutting of metallic and nonmetallic thin sheets is widely prevalent even in small scale industries as a flexible manufacturing tool. As for the laser welding is concerned, industrial applications are rather limited in mass production lines. This mainly comes from the fact that the present laser technologies have not employed the adaptive control because of the lack of sensors, monitoring, and control systems which can tolerate the high-precision and high-speed processing. In spite of this situation, laser welding is rapidly increasing in recent years in industries such as automotive, machinery, electric/electronic, steel, heavy industries, etc. Laser surface modification technologies have attracted significant interest from industrial people, but actual application is very limited today. However, the number of R&D papers is increasing year by year. The paper also reviews these new technology trends in Japan.
Distribution and impact of helminth diseases of livestock in developing countries (2016)

Distribution and impact of helminth diseases of livestock in developing countries , Distribution and impact of helminth diseases of livestock in developing countries , مرکز فناوری اطلاعات و اطلاع رسانی کشاورزی
Strain Differences in Response to Traumatic Brain Injury in Long-Evans Compared to Sprague-Dawley Rats (2009)

The selected strain of rodent used in experimental models of traumatic brain injury is typically dependent upon the experimental questions asked and the familiarity of the investigator with a specific rodent strain. This archival study compares the injury responsiveness and recovery profiles of two popular outbred strains, the Long-Evans (LE) and the Sprague-Dawley (SD), after brain injury induced by lateral fluid percussion injury (LFPI). General findings include a significantly longer duration of unconsciousness in LE rats, but similar durations of apnea. Both strains displayed the same level of initial FPI-induced behavioral deficits, followed by a more rapid rate of functional recovery in SD rats. Cortical volume loss was not significantly different, but close inspection of the data suggests the possibility that LE rats may be more susceptible to damage in the hemisphere contralateral to the injury site than are SD rats. It is hoped that the information provided here encourages greater attention to the subtle differences and similarities between strains in future pre-clinical efficacy studies of traumatic brain injury.
Comparative Evaluation of Information Dissemination Methods for Effective and Efficient Information Sharing in Wireless Sensor Networks (2011)

Wireless sensor networks (WSNs) consist of small　nodes with sensing, computation, and wireless communication capabilities.　Since overlaying multiple service-oriented networks on　a WSN wastes bandwidth and energy, we consider all-to-all type　information sharing in this paper. Although there have been various　proposals of mechanisms to disseminate information among　nodes in an efficient and effective manner, their performance has　evaluated under specific conditions. In this paper, we conducted　comprehensive evaluation of information dissemination methods　to clarify their comparative characteristics and the range of　application. Through simulation experiments, we showed that　tree-based methods could achieve high delivery ratio in a small　network, whereas a flooding-based or gossiping-based method　was more effective in large-scale and low-density networks.
<i>In Vivo</i>Introduction of Unpreferred Synonymous Codons Into the Drosophila<i>Adh</i>Gene Results in Reduced Levels of ADH Protein (2003)

The evolution of codon bias, the unequal usage of synonymous codons, is thought to be due to natural selection for the use of preferred codons that match the most abundant species of isoaccepting tRNA, resulting in increased translational efficiency and accuracy. We examined this hypothesis by introducing 1, 6, and 10 unpreferred codons into the Drosophila alcohol dehydrogenase gene (Adh). We observed a significant decrease in ADH protein production with number of unpreferred codons, confirming the importance of natural selection as a mechanism leading to codon bias. We then used this empirical relationship to estimate the selection coefficient (s) against unpreferred synonymous mutations and found the value (s >or= 10(-5)) to be approximately one order of magnitude greater than previous estimates from population genetics theory. The observed differences in protein production appear to be too large to be consistent with current estimates of the strength of selection on synonymous sites in D. melanogaster.
Specification, validation, and synthesis of email agent controllers (2000)

With a few exceptions, previous formal methods for reactive system design have focused on finite state machines represented in terms of boolean states and boolean next-state functions. By contrast, in many reactive system domains requirements engineers and developers think in terms of complex data types and expressive next-state functions. Formal methods for reactive system design must be extended to meet their needs as well. I term a reactive system function rich if expressing its state, next-state function, or output function naturally requires this higher expressive power. ISAT, a prototype formal-methods based tool environment, is intended to assist in the creation of function rich reactive systems. This paper describes a case study I have carried out using ISAT to design, validate, synthesize, and evolve controllers for the email agent components making up a novel spam-free email system that I deployed in a user trial in July 1999. The trial has been running since, with high availability, through several evolutionary specification changes and resulting software releases. In addition to summarizing ISAT and the trial, this paper discusses tool requirements placed by the domain and task, the simple and powerful platform/controller/pure-functions software architecture of the components, as well as lessons learned from the study.
Apparent mineralocorticoid excess, pseudohypoaldosteronism, and urinary electrolyte excretion: toward a redefinition of mineralocorticoid action (1990)

Patients with apparent mineralocorticoid excess (AME) have low or absent activity of the enzyme 11 beta OH steroid dehydrogenase (11SD), and inappropriately high intrarenal levels of cortisol resulting in Na+ retention and hypertension. Pseudohypoaldosteronism (PHA), in contrast, is characterized by salt wasting despite hyperaldosteronemia, reflecting low or absent mineralocorticoid receptors (MR). Although AME is presumed to reflect inappropriate cortisol occupancy of MR, several features also suggest inappropriate occupancy of glucocorticoid receptors (GR). To test this possibility, we administered carbenoxolone, which is known to block 11SD, to four patients with PHA, and observed marked mineralocorticoid effects, e.g., antinatriuresis and elevated plasma bicarbonate. To further test the possibility that occupancy of renal GR may induce a classical mineralocorticoid response, we administered the highly specific glucocorticoid RU 28362 to adrenalectomized rats and showed that it has profound antinatriuretic effects. Finally, by selectively blocking MR with RU 28318 or GR with RU 38486, we have shown that corticosterone, the physiologic glucocorticoid in rats, has an antinatriuretic effect in adrenalectomized rats via either MR or GR occupancy. Previous studies have clearly shown that MR are inherently nonselective and have equivalent intrinsic affinity for aldosterone, corticosterone, and cortisol. The present studies suggest that this nonselectivity includes the nuclear response element to which either MR or GR may bind to elicit a mineralocorticoid effect, and further underscore the importance of the enzyme 11SD in the specific mineralocorticoid action of aldosterone.
Possible role of tissue‐bound calcium ions in citrate‐mediated high‐temperature antigen retrieval (1994)

High-temperature preheating of sections in the presence of a salt (e.g., citrate) or a protein denaturant (e.g., urea) solution has been shown recently to provide a reliable alternative to tissue proteolysis for antigen retrieval from formaldehyde-fixed, paraffin-embedded tissues. However, the underlying mechanism of action of this form of pretreatment remains highly speculative. In this study, we show that calcium chelating agents such EDTA and EGTA are more effective than citrate in the retrieval of a citrate-sensitive nuclear antigen, Ki-67. Also, sodium carbonate and another calcium precipitating agent are both able to effect antigen retrieval at high temperatures. The overall data therefore suggest that either the chelation or the precipitation of tissue-bound calcium ions, and perhaps also other divalent metal cations, is a critical step in salt-mediated antigen retrieval. As a corollary, it is suggested that tight complexing of calcium ions or other divalent metal cations with proteins during formaldehyde tissue fixation is responsible for the masking of certain antigens.
Ultra-deep anisotropic etching of (110) silicon (1999)

The anisotropic etching behavior of (110) silicon wafers in KOH and TMAH was studied with emphasis on ultra-deep microchannels. Effects which degrade the etching behavior when etching to a depth of the order of a millimeter were encountered and investigated. In particular, oxygen precipitates and their growth during high temperature processing apparently strongly affect the etching of the (111) and (110) planes and reduce the achievable anisotropy ratio. A new 1300 °C high temperature step significantly reduces these negative effects by dissolving oxygen precipitates back into the crystal. Additionally, the influence of pattern alignment, solution concentration and the solution dissolved silicon content as well as the influence of varying masking layers on the achievable anisotropy ratio were investigated and optimized.
Polycystic Ovary Syndrome and Mental Health: A Review (2006)

After completion of this article, the reader should be able to explain that, in addition to physiologic changes, women with polycystic ovary syndrome (PCOS) have various mental health problems and lowered health-related quality of life issues and state that treatment must address these concerns.
Cardiolipin biosynthesis and remodeling enzymes are altered during development of heart failure (2008)

Cardiolipin (CL) is responsible for modulation of activities of various enzymes involved in oxidative phosphorylation. Although energy production decreases in heart failure (HF), regulation of cardiolipin during HF development is unknown. Enzymes involved in cardiac cardiolipin synthesis and remodeling were studied in spontaneously hypertensive HF (SHHF) rats, explanted hearts from human HF patients, and nonfailing Sprague Dawley (SD) rats. The biosynthetic enzymes cytidinediphosphatediacylglycerol synthetase (CDS), phosphatidylglycerolphosphate synthase (PGPS) and cardiolipin synthase (CLS) were investigated. Mitochondrial CDS activity and CDS-1 mRNA increased in HF whereas CDS-2 mRNA in SHHF and humans, not in SD rats, decreased. PGPS activity, but not mRNA, increased in SHHF. CLS activity and mRNA decreased in SHHF, but mRNA was not significantly altered in humans. Cardiolipin remodeling enzymes, monolysocardiolipin acyltransferase (MLCL AT) and tafazzin, showed variable changes during HF. MLCL AT activity increased in SHHF. Tafazzin mRNA decreased in SHHF and human HF, but not in SD rats. The gene expression of acyl-CoA: lysocardiolipin acyltransferase-1, an endoplasmic reticulum MLCL AT, remained unaltered in SHHF rats. The results provide mechanisms whereby both cardiolipin biosynthesis and remodeling are altered during HF. Increases in CDS-1, PGPS, and MLCL AT suggest compensatory mechanisms during the development of HF. Human and SD data imply that similar trends may occur in human HF, but not during nonpathological aging, consistent with previous cardiolipin studies.
Orally Active Peptidic Bradykinin B<sub>1</sub> Receptor Antagonists Engineered from a Cyclotide Scaffold for Inflammatory Pain Treatment (2012)

Edible: By grafting natural peptide antagonists onto the cyclotide kalata B1, orally active peptides were engineered, which are potentially useful therapeutics for the treatment of inflammatory pain. For example, the entire loop 6 of kalata B1 was replaced with the peptidic bradykinin B1 receptor antagonist DALK (red in scheme) to obtain the cyclic bradykinin antagonist ckb-kal.
Competition from the Commons? (2009)

2006 had been a very interesting, not to say turbulent, year for Juergen Bauer, head of product strategy for small and medium-sized enterprises for Siemens Enterprise Communications (SEN), and all of what had previously been Siemens Communications. With the foundation of the new SEN subsidiary that originated from the Enterprise Networks segment of Siemens Communications, SEN could now focus on what lay ahead, hoping to leave its troubled past behind for good. Sitting in his Munich office in late December, Bauer was starting to prepare a presentation he was supposed to give at the first Board meeting in January 2007, in which the current strategy of SEN was to be reviewed. Bauer had chosen to take a closer look at some of the current drivers of the industry – especially Voice over IP (VoIP) – and how they were currently being addressed by SEN.
Construction and Characterization of Single-Chain Variable Fragment Antibody Library Derived from Germline Rearranged Immunoglobulin Variable Genes (2011)

Antibody repertoires for library construction are conventionally harvested from mRNAs of immune cells. To examine whether germline rearranged immunoglobulin (Ig) variable region genes could be used as source of antibody repertoire, an immunized phage-displayed scFv library was prepared using splenocytic genomic DNA as template. In addition, a novel frame-shifting PCR (fsPCR) step was introduced to rescue stop codon and to enhance diversity of the complementarity-determining region 3 (CDR3). The germline scFv library was initially characterized against the hapten antigen phenyloxazolone (phOx). Sequence analysis of the phOx-selective scFvs indicated that the CDRs consisted of novel as well as conserved motifs. In order to illustrate that the diversity of CDR3 was increased by the fsPCR step, a second scFv library was constructed using a single scFv clone L3G7C as a template. Despite showing similar binding characteristics towards phOx, the scFv clones that were obtained from the L3G7C-derived antibody library gave a lower non-specific binding than that of the parental L3G7C clone. To determine whether germline library represented the endogenous immune status, specific scFv clones for nucleocapsid (N) protein of SARS-associated coronavirus (SCoV) were obtained both from naïve and immunized germline scFv libraries. Both libraries yielded specific anti-N scFvs that exhibited similar binding characteristics towards recombinant N protein, except the immunized library gave a larger number of specific anti-N scFv, and clones with identical nucleotide sequences were found. In conclusion, highly diversified antibody library can be efficiently constructed using germline rearranged immunoglobulin variable genes as source of antibody repertoires and fsPCR to diversify the CDR3.
DF-DD for channels with phase noise (2003)

In this letter, we design decision-feedback differential detection (DF-DD) schemes for channels with phase noise. If the DF-DD feedback filter is properly optimized, a performance similar to that of a more complex scheme, recently reported by Chiavaccini and Vitetta, based on expectation maximization, can be achieved. However, it is also shown that an error floor is unavoidable for channels with phase noise. If a constraint is introduced, the DF-DD receiver can be made robust against unknown frequency offsets.
Modulating early visual processing by language (2017)

It is commonly assumed that language refers to high-level visual concepts while leaving low-level visual processing unaffected. This view dominates the current literature in computational models for language-vision tasks, where visual and linguistic input are mostly processed independently before being fused into a single representation. In this paper, we deviate from this classic pipeline and propose to modulate the \emph{entire visual processing} by linguistic input. Specifically, we condition the batch normalization parameters of a pretrained residual network (ResNet) on a language embedding. This approach, which we call MOdulated RESnet (\MRN), significantly improves strong baselines on two visual question answering tasks. Our ablation study shows that modulating from the early stages of the visual processing is beneficial.
Small molecule splicing modifiers with systemic HTT-lowering activity (2021)

Huntington's disease (HD) is a hereditary neurodegenerative disorder caused by expansion of cytosine-adenine-guanine (CAG) trinucleotide repeats in the huntingtin (HTT) gene. Consequently, the mutant protein is ubiquitously expressed and drives pathogenesis of HD through a toxic gain-of-function mechanism. Animal models of HD have demonstrated that reducing huntingtin (HTT) protein levels alleviates motor and neuropathological abnormalities. Investigational drugs aim to reduce HTT levels by repressing HTT transcription, stability or translation. These drugs require invasive procedures to reach the central nervous system (CNS) and do not achieve broad CNS distribution. Here, we describe the identification of orally bioavailable small molecules with broad distribution throughout the CNS, which lower HTT expression consistently throughout the CNS and periphery through selective modulation of pre-messenger RNA splicing. These compounds act by promoting the inclusion of a pseudoexon containing a premature termination codon (stop-codon psiExon), leading to HTT mRNA degradation and reduction of HTT levels.