gebhart/patrepeval huggingface dataset:
MicroRNA mir-346 targets the 5′-untranslated region of receptor-interacting protein 140 (RIP140) mRNA and up-regulates its protein expression (2009)

RIP140 (receptor-interacting protein 140) is a transcriptional co-repressor that regulates diverse genes such as those responsive to hormones and involved in metabolic processes. The expression of RIP140 is regulated by multiple hormonal activities in adipose tissue and cancer cell lines. However, it is unclear whether and how RIP140 is regulated post-transcriptionally. Using 5'RACE (rapid amplification of 5' cDNA ends), we have identified a novel 5' splice variant of RIP140 mRNA in mouse brain and P19 cells. A target sequence for miRNA (microRNA) mir-346 was found in the 5'UTR (5'-untranslated region) of RIP140 mRNA; this miRNA is also expressed endogenously in mouse brain and P19 cells. Gain- and loss-of-function studies demonstrated that mir-346 elevates RIP140 protein levels by facilitating association of its mRNA with the polysome fraction. Furthermore, the activity of mir346 does not require Ago-2 (Argonaute 2). The expression of mir-346 enhances the gene repressive activity of RIP140. This is the first report demonstrating post-transcriptional regulation of RIP140 mRNA, involving the enhancing effect of a specific miRNA that targets RIP140's 5'UTR.
Recovery and tracking of continuous 3D surfaces from stereo data using a deformable dual-mesh (1999)

We propose a novel method for continuous 3D depth recovery and tracking using calibrated stereo. The method integrates stereo correspondence, surface reconstruction and tracking by using a new single deformable dual mesh optimization, resulting in simplicity, robustness and efficiency. In order to combine stereo correspondence and structure recovery, the method introduces an external energy function defined for a 3D volume based on cross-correlation between the stereo pairs. The internal energy functional of the deformable dual mesh imposes smoothness on the surfaces and it serves as a communication tool between the two meshes. Under the forces produced by the energy terms, the dual mesh deforms to recover and track the 3D surface. The newly introduced dual-mesh model, which is one of the main contributions of this paper, makes the system robust against local minima and yet it is efficient. A coarse-to-fine minimization approach makes the system even more efficient. Tracking is achieved by using the recovered surface as an initial position for the next time frame. Although the system can effectively utilize initial surface positions and disparity data, they are not needed for a successful operation, which makes this system applicable to a wide range of areas. We present the results of a number of experiments on stereo human face and cloud images, which proves that our new method is very effective.
Biosynthesis of <i>Staphylococcus aureus</i> Autoinducing Peptides by Using the <i>Synechocystis</i> DnaB Mini-Intein (2007)

The Agr quorum-sensing system of Staphylococcus aureus modulates the expression of virulence factors in response to autoinducing peptides (AIPs). The peptides are seven to nine residues in length and have the C-terminal five residues constrained in a thiolactone ring. We have developed a new method to generate AIP structures using an engineered DnaB mini-intein from Synechocystis sp. strain PCC6803. In the method, an oligonucleotide encoding the AIP is ligated to the intein and the fusion protein is expressed and purified by affinity chromatography. To produce the correct AIP structure, intein splicing is interrupted, allowing the cysteine side chain to catalyze thiolactone ring formation and release AIP from the resin. The technique is simple and robust, and we have successfully produced the three main classes of AIPs using the intein system. The intein-generated AIPs possessed the correct thiolactone ring modification based on biochemical analysis, and, importantly, all the samples were bioactive against S. aureus. The AIP activity was confirmed through Agr interference and activation profiling with developed S. aureus reporter strains. The simplicity of the method, benefits of DNA encoding, and scalable nature enable the production of S. aureus AIPs for many biological applications.
Paired Arcuate Keratotomy (1988)

Twenty-five cadaver eyes were used to study the effect of paired arcuate keratotomy on corneal astigmatic changes. Paired arcuate incisions placed at optical zones of 5, 6, 7, 8, and 9 mm were progressively lengthened from 45 degrees to 60 degrees, 90 degrees, and, finally, 120 degrees. The corneal flattening in the meridian centered over the incisions and the corneal steepening 90 degrees away were quantified with each successive lengthening. Linear regression analysis showed a direct linear relationship of corneal astigmatic change (sum of corneal flattening and steepening, or delta K) to decreasing optical zone size as measured in millimeters and increasing incision length as measured in degrees. The delta K value ranged from 2.65 +/- 1.07 diopters to 22.05 +/- 3.55 D. The flattening/steepening coupling ratio mean was 1.47 +/- 0.41. Progressively longer paired arcuate incisions produced a predictable and titratable corneal flattening in the meridian centered over the incisions and a slightly smaller corneal steepening 90 degrees away, making the procedure ideal for mixed astigmatism.
A dynamic program analysis to find floating-point accuracy problems (2012)

Programs using floating-point arithmetic are prone to accuracy problems caused by rounding and catastrophic cancellation. These phenomena provoke bugs that are notoriously hard to track down: the program does not necessarily crash and the results are not necessarily obviously wrong, but often subtly inaccurate. Further use of these values can lead to catastrophic errors.
Efficacy of androgen deprivation therapy (ADT) in patients with advanced prostate cancer (2008)

In this large, retrospective study of HSPC patients in a medical oncology practice treated with ADT for nonlocalized prostate cancer, we found factors predicting efficacy of this treatment differed based on whether metastases were present at ADT initiation. The use of ADT as a part of local therapy was associated with a significantly decreased TTP, regardless of metastatic disease status.
Traumatic Inferior Vena Caval Injuries (1994)

Twenty-three cases of inferior vena caval injury (1.4% of all operatively managed abdominal injuries) are reviewed. The caval injury presented as free haemorrhage in 15 cases and as a retroperitoneal haematoma in eight. The site of vena caval injury was at or above the level of the renal veins in 14 cases (61%). Successful lateral suture repair was achieved in 18 cases (78%). The overall mortality rate was 39%. Factors positively associated with survival were stab wound, presentation as retroperitoneal haematoma, infrarenal injury, low Abdominal Trauma Index score and small peroperative blood loss. Concomitant injury to the abdominal aorta, liver or kidney worsened the prognosis. The crucial factor in management of inferior vena caval injuries is rapid and effective control of bleeding, whether from the caval or associated injuries.
The Prevalence of Dementia in Down Syndrome (1996)

The prevalence of clinical dementia was assessed in three age groups of patients with Down syndrome in the county of Aarhus, Denmark: Group 1: 14-16 years (n = 13), group 2: 23-29 years (n = 34), group 3: 50-60 years (n = 25). Seventy-two (85%) of 85 patients participated. Caregivers were interviewed and a neurological examination was performed. An EEG was recorded in 50 patients. Definite clinical dementia was defined as an acquired and progressive decline in 4 or more out of 17 items that are considered to indicate dementia in Down syndrome. Possible dementia was considered when 1-3 items were affected. Six (24%) in group 3 had definite clinical dementia. A further 6 patients in group 3 and 2 (6%) in group 2 had possible dementia. This is the first population-based study with a clinical assessment of the prevalence of dementia in Down syndrome.
Highly Purified Pheophorbide A As A Photosensitizer In Human Bladder Carcinoma In Vitro (1988)

A method was developed for preparing highly purified pheophorbide a using the blue-green alga Anacystis nidulans as a source of chlorophyll a which was subsequently converted to the desired compound using a cation-exchange resin (Dowex 50Wx4, H+ -form) as a proton source. Pheophorbide a was found to be 20 times more photocytotoxic than was hematoporphyrin (under red light >560 nm) against EJ cells (a cell line established from a human transitional cell carcinoma of the bladder) in vitro. Pheophorbide a accumulated rapidly in EJ and IMR-90 (a non-neoplastic cell line established from human fibroblasts) cells, reaching the maximum by 30 minutes. However, the number of EJ cells fluorescing at 5, 15 and 30 minutes was 1.7, 1.5 and 1.2 times greater than IMR-90 cells respectively. Moreover, only 17 percent of IMR-90 versus 75 percent of EJ cells fluoresced at 48 hours following 4-hour pheophorbide a exposure. These results indicate that pheophorbide a is highly photocytotoxic for EJ cells in vitro and undergoes differential uptake and retention in neoplastic as compared with non-neoplastic cells.
The actin-based motor protein myosin II regulates MHC class II trafficking and BCR-driven antigen presentation (2007)

Antigen (Ag) capture and presentation onto major histocompatibility complex (MHC) class II molecules by B lymphocytes is mediated by their surface Ag receptor (B cell receptor [BCR]). Therefore, the transport of vesicles that carry MHC class II and BCR-Ag complexes must be coordinated for them to converge for processing. In this study, we identify the actin-associated motor protein myosin II as being essential for this process. Myosin II is activated upon BCR engagement and associates with MHC class II-invariant chain complexes. Myosin II inhibition or depletion compromises the convergence and concentration of MHC class II and BCR-Ag complexes into lysosomes devoted to Ag processing. Accordingly, the formation of MHC class II-peptides and subsequent CD4 T cell activation are impaired in cells lacking myosin II activity. Therefore, myosin II emerges as a key motor protein in BCR-driven Ag processing and presentation.
Molecular imaging in prostate cancer (2003)

Prostate cancer (PCa) is the most common non-cutaneous malignancy in men. New ways to diagnose this cancer in its early stages are needed. Unique genetic and biochemical changes in the cell pave the way for tumors to grow and metastasize. Novel imaging approaches attempt to detect pathological processes in cancer cells at the molecular level. This has led to the establishment and development of the field of molecular imaging. Positron emission tomography (PET), magnetic resonance spectroscopic imaging (MRSI), magnetic resonance imaging (MRI), and radiolabeled antibodies are a few of the modalities that can detect abnormal tumor metabolic processes in the clinical setting. Other imaging techniques are still in their early phase of development but hold promise for the future, including bioluminescence imaging (BLI), measurement of tumor oxygenation, and measurement of uptake of iodine by tumors. These techniques are non-invasive and can spare the patient undue morbidity, while potentially providing early diagnosis, accurate follow-up and, finally, valuable prognostic information.
High frame rate for 3D Time-of-Flight cameras by dynamic sensor calibration (2011)

3D Time-of-Flight cameras are able to deliver robust depth maps of dynamic scenes. The frame rate, however, is limited because today's systems utilizing two-tap sensors need to acquire the required raw images in multiple instances in order to compute one depth map. These multiple raw images allow canceling out systematic errors introduced by asymmetries in the two taps, which otherwise would distort the reconstructed depth map. This work presents a method to implicitly calibrate these asymmetries of multi-tap 3D Time-of-Flight sensors. The calibration data are gathered from arbitrary live acquisitions possibly in real-time. The proposed correction of raw data supersedes the commonly used averaging technique. Thus it is possible to compute multiple depth maps from a single set of raw images. This increases the frame rate by at least a factor of two. The method is verified using real camera data and is evaluated quantitatively.
<i>Francisella tularensis</i>Type A Strains Cause the Rapid Encystment of<i>Acanthamoeba castellanii</i>and Survive in Amoebal Cysts for Three Weeks Postinfection (2009)

Francisella tularensis, the causative agent of the zoonotic disease tularemia, has recently gained increased attention due to the emergence of tularemia in geographical areas where the disease has been previously unknown and to the organism's potential as a bioterrorism agent. Although F. tularensis has an extremely broad host range, the bacterial reservoir in nature has not been conclusively identified. In this study, the ability of virulent F. tularensis strains to survive and replicate in the amoeba Acanthamoeba castellanii was explored. We observe that A. castellanii trophozoites rapidly encyst in response to F. tularensis infection and that this rapid encystment phenotype is caused by factor(s) secreted by amoebae and/or F. tularensis into the coculture medium. Further, our results indicate that in contrast to the live vaccine strain LVS, virulent strains of F. tularensis can survive in A. castellanii cysts for at least 3 weeks postinfection and that the induction of rapid amoeba encystment is essential for survival. In addition, our data indicate that pathogenic F. tularensis strains block lysosomal fusion in A. castellanii. Taken together, these data suggest that interactions between F. tularensis strains and amoebae may play a role in the environmental persistence of F. tularensis.
Dipeptidyl peptidase IV on activated T cells as a target molecule for therapy of rheumatoid arthritis (2003)

The extracellular domain of the T cell co-stimulatory molecule CD26 possesses dipeptidyl peptidase IV (DP IV) enzyme activity. Activated T cells are known to increase expression of cell surface DP IV and some specific inhibitors of this enzyme have been reported to suppress T cell function. Previously we have identified a DP IV inhibitor, designated TMC-2, found in culture supernatant of Aspergillus oryzae. Administration of TMC-2 to rats with adjuvant arthritis caused marked suppression of paw swelling. To elucidate the mechanism of TMC-2 antiarthritic activity, we have studied its effects on T cell function. Here we show that TMC-2 inhibited DP IV activity of CD26 immunoprecipitated from T cell lysates, and also inhibited proliferative responses of T cells to specific antigen or anti-CD3 antibody. Suppression of IL-2 production was demonstrated at both the mRNA and protein levels. TMC-2 did not alter the PTPase activity of pure CD45, but when this molecule was co-precipitated from T cell lysates together with associated CD26, its PTPase was virtually completely abolished by TMC-2. These results suggest that modulation of CD45 PTPase activity might be responsible for functional suppression of T cells by TMC-2. Because the effects of TMC-2 on T cells were reversible and it was not toxic at the concentrations used, TMC-2 may be a candidate novel therapeutic agent for rheumatoid arthritis.
Oracle SAP Administration (1999)

From the Publisher:
SAP is the leading vendor of enterprise resource planning (ERP) systems in the world. (The name SAP is an acronym for the German Systemanalyse und Programmentwicklung, which roughly translates to Systems, Applications, and Products in Data Processing.) Developed and marketed by SAP-AG, a Germany company that was founded in 1972 by IBM application developers, SAP has historically sold to the European market. During the 1990s, the company has increasingly dominated the U.S. market as well among large Fortune 500 companies. Nearly half the SAP user base is now in the U.S. Now that SAP-AG is beginning to penetrate the small to medium-size companies, client/server sales are accelerating. 
The SAP system performs a wide range of business functions, from manufacturing, sales, and distribution to accounting and human resources. By linking together these business functions, SAP helps the entire enterprise run more smoothly. The system can be used with virtually any hardware or operating system and with most database systems. Oracle is the dominant DBMS - about 80% of SAP systems use Oracle. Conversely, about 20% of large Oracle sites run SAP -- and the numbers are growing. Although overall SAP numbers are tightly guarded, it appears that there are about 20,000 SAP sites, in 90 countries. SAP-AG's 1998 sales were approximately 8.47 billion. 
Although there is voluminous documentation on using SAP and using Oracle, until now there has been no book that described the intersection between the two systems. Experienced Oracle administrators have a lot to learn when their organizations start using SAP. Oracle SAP administration differs from traditional Oracle administration in many ways. SAP provides its own tools for Oracle administration; Oracle DBAs need to learn how to use these tools -- and need to learn when the tools are not the best way to accomplish a task. There are special settings for initialization (INIT.ORA) parameters, special monitoring and tuning guidelines, and a variety of other special situations. 
This concise book is aimed at experienced Oracle database administrators, system administrators, and developers who are using either Oracle8 or Oracle7. It emphasizes the differences between traditional Oracle administration and Oracle/SAP administration, and it supplements the Oracle and SAP documentation. The book covers the most useful administration tools, SAPDBA and SAPGUI. It provides recommendations for the most efficient placement of data files; monitoring databases; reorganizing tables, tablespaces, and indexes; backing up and recoving databases; and tuning Oracle/SAP databases for best performance. There are chapters on special issues for parallel processing and for very large SAP databases and a summary of additional resources for the Oracle/SAP administrator. The tried-and-true tips and techniques contained in this book should save you hundreds of hours of aggravation while you adapt to using Oracle and SAP in combination.
Adhesion Molecule–dependent Mechanisms Regulate the Rate of Macrophage Clearance During the Resolution of Peritoneal Inflammation (2002)

Macrophage clearance is essential for the resolution of inflammation. Much is known about how monocytes enter the inflammatory site but little is known about how resultant macro-phages are cleared. We have previously demonstrated that macrophage clearance from resolving peritonitis occurs by emigration into draining lymphatics rather than local apoptosis. We now examine mechanisms for this process, in particular by evaluating the hypothesis that modulation of adhesion interactions between macrophages and cells lining the lymphatics regulates the rate of macrophage clearance. We demonstrate in vivo that macrophages adhere specifically to mesothelium overlying draining lymphatics and that their emigration rate is regulated by the state of macrophage activation. We observed that macrophage-mesothelial adhesion is Arg-Gly-Asp (RGD) sensitive and partially mediated by very late antigen (VLA)-4 and VLA-5 but not alpha(v) or beta(2) integrins. Moreover, macrophage clearance into lymphatics can be blocked in vivo by RGD peptides and VLA-4 and VLA-5 but not beta(2) blocking antibodies. This is the first evidence that macrophage emigration from the inflamed site is controlled and demonstrates that this is exerted through specific adhesion molecule regulation of macrophage-mesothelial interactions. It highlights the importance of adhesion molecules governing entry of cells into the lymphatic circulation, thus opening a new avenue for manipulating the resolution of inflammation.
Effects of Tris(tert-pentoxy)silanol Purge Time on SiO2 Thin-Film Growth Rate in Rapid Atomic Layer Deposition (2013)

Unusual growth per cycle (GPC) behaviors, depending on the tris(tert-pentoxy)silanol purge time, were observed in catalytic SiO2 growth by atomic layer deposition (ALD). Short purge times led to decreases in GPC, and normal saturated GPC was observed for longer purge times, following ideal ALD behavior. When an extremely long purge time was used, a decreased growth rate was observed; loss of surface hydroxyl groups as a result of increased cross-linking was considered to be a possible cause. SiO2 films of comparable quality to those obtained using longer purge times were obtained by increasing the Ar flow rate during purging.
An Operating Environment for the Jellybean Machine (1988)

The Jellybean Machine is a scalable MIMD concurrent processor consisting of special purpose RISC processors loosely coupled into a low latency network. I have developed an operating system to provide the supportive environment required to efficiently coordinate the collective power of the distributed processing elements. The system services are developed in detail, and may be of interest to other designers of fine grain, distributed memory processing networks.
Benchmarking simple database operations (1987)

There are two widely-known benchmarks for database management systems the TP1 benchmarks (Anon et al [1985]), designed to measure transaction throughout, and the Wisconsin benchmarks (Bitton, Dewitt, & Turbyfil [1984]), designed to measure the performance of a relational query processor. In our work with databases on engineering workstations, we found neither of these benchmarks a suitable measure for our applications' needs. Instead, our requirements are for response time for simple queries. We propose benchmark measurements to measure response time, specifically designed for the simple, object-oriented queries that engineering database applications perform. We report results from running this benchmark against some database systems we use ourselves, and provide enough detail for others to reproduce the benchmark measurements on other relational, object-oriented, or specialized database systems. We discuss a number of factors that make an order of magnitude improvement in benchmark performance caching the entire database in main memory, avoiding query optimization overhead, using physical links for prejoins, and using an alternative to the generally-accepted database “server” architecture on distributed networks.
Cochlear SGN neurons elevate pain thresholds in response to music (2021)

The C-tactile (CLTM) peripheral nervous system is involved in social bonding in primates and humans through its capacity to trigger the brain's endorphin system. Since the mammalian cochlea has an unusually high density of similar neurons (type-II spiral ganglion neurons, SGNs), we hypothesise that their function may have been exploited for social bonding by co-opting head movements in response to music and other rhythmic movements of the head in social contexts. Music provides one of many cultural behavioural mechanisms for 'virtual grooming' in that it is used to trigger the endorphin system with many people simultaneously so as to bond both dyadic relationships and large groups. Changes in pain threshold across an activity are a convenient proxy assay for endorphin uptake in the brain, and we use this, in two experiments, to show that pain thresholds are higher when nodding the head than when sitting still.