gebhart/patrepeval huggingface dataset:
The Interactomes of Influenza Virus NS1 and NS2 Proteins Identify New Host Factors and Provide Insights for ADAR1 Playing a Supportive Role in Virus Replication (2013)

Influenza A NS1 and NS2 proteins are encoded by the RNA segment 8 of the viral genome. NS1 is a multifunctional protein and a virulence factor while NS2 is involved in nuclear export of viral ribonucleoprotein complexes. A yeast two-hybrid screening strategy was used to identify host factors supporting NS1 and NS2 functions. More than 560 interactions between 79 cellular proteins and NS1 and NS2 proteins from 9 different influenza virus strains have been identified. These interacting proteins are potentially involved in each step of the infectious process and their contribution to viral replication was tested by RNA interference. Validation of the relevance of these host cell proteins for the viral replication cycle revealed that 7 of the 79 NS1 and/or NS2-interacting proteins positively or negatively controlled virus replication. One of the main factors targeted by NS1 of all virus strains was double-stranded RNA binding domain protein family. In particular, adenosine deaminase acting on RNA 1 (ADAR1) appeared as a pro-viral host factor whose expression is necessary for optimal viral protein synthesis and replication. Surprisingly, ADAR1 also appeared as a pro-viral host factor for dengue virus replication and directly interacted with the viral NS3 protein. ADAR1 editing activity was enhanced by both viruses through dengue virus NS3 and influenza virus NS1 proteins, suggesting a similar virus-host co-evolution.
Alternative splicing of β-galactosidase mRNA generates the classic lysosomal enzyme and a β-galactosidase-related protein (1989)

We have isolated two cDNAs encoding human lysosomal beta-galactosidase, the enzyme deficient in GM1-gangliosidosis and Morquio B syndrome, and a beta-galactosidase-related protein. In total RNA from normal fibroblasts a major mRNA of about 2.5 kilobases (kb) is recognized by cDNA probes. A minor transcript of about 2.0 kb is visible only in immunoselected polysomal RNA. A heterogeneous pattern of expression of the 2.5-kb beta-galactosidase transcript is observed in fibroblasts from different GM1-gangliosidosis patients. The nucleotide sequences of the two cDNAs are extensively colinear. However, the short cDNA misses two noncontiguous protein-encoding regions (1 and 2) present in the long cDNA. The exclusion of region 1 in the short molecule introduces a frameshift in its 3'-flanking sequence, which is restored by the exclusion of region 2. These findings imply the existence of two mRNA templates, which are read in a different frame only in the nucleotide stretch between regions 1 and 2. Sequence analysis of genomic exons of the beta-galactosidase gene shows that the short mRNA is generated by alternative splicing. The long and short cDNAs direct the synthesis in COS-1 cells of beta-galactosidase polypeptides of 85 and 68 kDa, respectively. Only the long protein is catalytically active under the assay conditions used, and it is capable of correcting beta-galactosidase activity after endocytosis by GM1-gangliosidosis fibroblasts. The subcellular localization of cDNA-encoded beta-galactosidase and beta-galactosidase-related proteins is different.
Validation of Delft3D as a Coastal Surge and Inundation Prediction System (2016)

Abstract : Coastal regions are vital to naval operations and have rapidly growing populations making them increasingly vulnerable to storm surge and inundation. The US Navy currently uses the Delft3D modeling suite (Stelling, 1996) for predicting nearshore circulation when inundation is not the primary concern, and PCTides for surge modeling. This report will detail the validation of the new Coastal Surge and Inundation Prediction System (CSIPS) based on Delft3D for operational use by the US Navy. Baseline studies using re-analysis winds during Hurricanes Ike and Irene as well as some sensitivity studies are presented. We also compare the results from Delft3D and PCTides in an operational scenario to available data.
Relationship of ethnicity and CD4 Count with glucose metabolism among HIV patients on Highly-Active Antiretroviral Therapy (HAART) (2013)

Among hypertriglyceridemic HIV patients on HAART, African-Americans and Hispanics are at increased risk of developing diabetes. Ethnicity also interacts with CD4+ T cell count attained on stable HAART to affect post-challenge glycemic response.
Development and Field Testing of a Novel Multifunctional Drilling Enhancement Tool in a Middle East Field (2020)

Well drilling and wellbore conditioning typically involve multiple specialized drilling tools. Systematic application of such tools can be a challenge from a logistics and maintenance perspective, which eventually has an impact on the efficiency of the drilling process as well as the resulting wellbore condition. This paper presents a new multifunctional drilling tool developed to address such operational challenges. The tool’s effect on the drilling and logging process is illustrated through a field case study. The CRS is a multifunctional drilling tool able to Cut, Ream and Stabilize when installing in a BHA. It is envisioned as an integral bottom hole assembly (BHA) component replacing the uppermost stabilizer while selectively acting as a fixed blade cutter, roller-reamer, lateral vibration damper, friction reducer, stabilizer and/or key-seat wiper. The specific function is dependent on wellbore conditions and is passively activated or engaged during operation. The CRS was successfully field-tested in a middle east field late 2018. Offset well data were used to validate the effectiveness of the tool and provide recommendations for future development. An offset well was used as a benchmark for comparison to characterize CRS performance. The CRS replaced the stabilizer directly above the measurement while drilling (MWD) tools as part of the BHA used for drilling the interval from 1800 to 2520 meters. When compared to the offset well, the tool had no negative effect on trajectory or dogleg severity. Tight spots required significant back-reaming in the offset well during pull-out-of-hole (POOH). Using the CRS saved 63 hours of rig time when POOH due to the tool’s effective tight spot cutting capability. High torque fluctuations ranging between 2 to 13 klbs-ft were observed in the offset well while drilling formations mainly composed of sticky claystone and limestone. The resulting poor wellbore quality rendered significant logging challenges. The CRS’s ability to damp lateral vibration while engaging in its reaming function resulted in the mitigation of these challenges. Another innovative feature of the CRS’s reaming function is the complete elimination of cutter loss risk. The CRS body is, by far, the industry’s largest area bearing mounted reaming structure and its concentric design eliminates the possibility of it being lost in the hole. The CRS body rotates in response to lateral vibration and drill string whirl when in a vertical or deviated wellbore, effectively contributing to the damping of both vibration modes. The body acts as friction reducer at high deviations. The rotating body also translates on the tool mandrel when faced with a tight spot or pack-off. This translation is opposed by a unique spring assembly that can deliver full top drive torque to the body to cut through the formation.
Role of Hepatocyte Growth Factor in the Immunomodulation Potential of Amniotic Fluid Stem Cells (2015)

New information about the secretome pattern is reported in this paper. Human amniotic fluid stem cells (hAFSCs) possess immunomodulatory properties involving hepatocyte growth factor production. hAFSCs could be used in immunotherapies and might be able to avoid allogenic rejection.
The von Hippel–Lindau tumour suppressor interacts with microtubules through kinesin‐2 (2007)

Synthesis and maintenance of primary cilia are regulated by the von Hippel-Lindau (VHL) tumour suppressor protein. Recent studies indicate that this regulation is linked to microtubule-dependent functions of pVHL such as orienting microtubule growth and increasing plus-end microtubule stability, however little is known how this occurs. We have identified the kinesin-2 motor complex, known to regulate cilia, as a novel and endogenous pVHL binding partner. The interaction with kinesin-2 facilitates pVHL binding to microtubules. These data suggest that microtubule-dependent functions of pVHL are influenced by kinesin-2.
Impacts of Energy Flexibility in Transactive Energy Systems With Large-Scale Renewable Generation (2022)

Modern-day energy systems are evolving to be complex, interconnected, and transactive systems without clear demarcation between energy “producers” and “consumers”. This is aided by the large-scale proliferation of renewables (at a centralized scale and in more distributed settings, such as rooftop solar) and the growing potential for demand-side flexibility. In this paper, we propose a mathematical framework that considers the interaction of energy flexibility and renewable generation in a transactive power system, where a grid operator can secure both generation and flexibility (storage) from centralized and/or distributed assets. Our results, derived under network-abstracted settings, mathematically relate the system operating cost to the available flexibility capacity. In addition, our proposed framework also characterizes the inflection point beyond which further addition of flexibility capacity does not affect the cost of system operation. Furthermore, the relationship between the price spread in the grid, i.e., the difference between maximum and minimum prices over the time horizon under consideration, and the available flexibility is also commented upon. Finally, we demonstrate our findings on a modified IEEE 30 bus test network.
Planar embedded pick-up coil sensor for integrated power electronic modules (2004)

This paper proposes a planar embedded structure pick-up coil current sensor for integrated power electronic modules technology. It has compact size, excellent linearity, stability, noise immunity and wide bandwidth without adding significant losses or parasitics. Preliminary test results and discussions are presented in this paper.
Imaging Prostate Cancer: A Multidisciplinary Perspective (2007)

The major goal for prostate cancer imaging in the next decade is more accurate disease characterization through the synthesis of anatomic, functional, and molecular imaging information. No consensus exists regarding the use of imaging for evaluating primary prostate cancers. Ultrasonography is mainly used for biopsy guidance and brachytherapy seed placement. Endorectal magnetic resonance (MR) imaging is helpful for evaluating local tumor extent, and MR spectroscopic imaging can improve this evaluation while providing information about tumor aggressiveness. MR imaging with superparamagnetic nanoparticles has high sensitivity and specificity in depicting lymph node metastases, but guidelines have not yet been developed for its use, which remains restricted to the research setting. Computed tomography (CT) is reserved for the evaluation of advanced disease. The use of combined positron emission tomography/CT is limited in the assessment of primary disease but is gaining acceptance in prostate cancer treatment follow-up. Evidence-based guidelines for the use of imaging in assessing the risk of distant spread of prostate cancer are available. Radionuclide bone scanning and CT supplement clinical and biochemical evaluation (prostate-specific antigen [PSA], prostatic acid phosphate) for suspected metastasis to bones and lymph nodes. Guidelines for the use of bone scanning (in patients with PSA level > 10 ng/mL) and CT (in patients with PSA level > 20 ng/mL) have been published and are in clinical use. Nevertheless, changes in practice patterns have been slow. This review presents a multidisciplinary perspective on the optimal role of modern imaging in prostate cancer detection, staging, treatment planning, and follow-up.
A case of long-term follow-up of a Japanese patient with Fabry disease without recurrent cerebral infarction treated with enzyme replacement therapy (2021)

35 歳男性．幼少期から両側大腿に皮疹があり，発汗障害，四肢の疼痛がみられた．また，これらの症状は運動や暑い気候で誘発された．2012年4月，急性発症の右顔面・上下肢麻痺，構音障害を呈し，頭部MRIで左レンズ核から放線冠にかけて急性期梗塞を認めた．幼少期の病歴と若年性脳梗塞であること，αガラクトシダーゼ活性低値，αガラクトシダーゼ遺伝子解析での2塩基の欠失からファブリー病（古典型）と診断し，アガルシダーゼαによる加療を開始した．治療後，四肢の疼痛や発汗障害は改善し，約8年半の間，脳梗塞の再発なく経過している．早期の酵素補充療法開始が，約8年半と長期にわたるファブリー病の脳血管障害再発予防に寄与したものと考えられた．
Controlling the Crystal Growth of Dodecasil 3C by Buffering with DL‐Histidine (2008)

Abstract Dodecasil 3C, a pure silica zeolite with an MTN‐type structure, was prepared by liquid‐phase hydrothermal synthesis in the presence of the amino acid dl ‐histidine. This compound acts as a buffer and affects the growth of zeolite, in particular its aggregation behaviour and particle size. As a result of the alteration the amino acid exerts on the silica chemistry in aqueous solution, nucleation was lowered and dodecasil 3C was formed as large, single crystals with sizes up to 140 μm.(© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2008)
Conserved Arginines at the P-Protein Stalk Binding Site and the Active Site Are Critical for Ribosome Interactions of Shiga Toxins but Do Not Contribute to Differences in the Affinity of the A1 Subunits for the Ribosome (2016)

The A1 subunits of Shiga toxin 1 (Stx1A1) and Shiga toxin 2 (Stx2A1) interact with the conserved C termini of ribosomal-stalk P-proteins to remove a specific adenine from the sarcin/ricin loop. We previously showed that Stx2A1 has higher affinity for the ribosome and higher catalytic activity than Stx1A1. To determine if conserved arginines at the distal face of the active site contribute to the higher affinity of Stx2A1 for the ribosome, we mutated Arg172, Arg176, and Arg179 in both toxins. We show that Arg172 and Arg176 are more important than Arg179 for the depurination activity and toxicity of Stx1A1 and Stx2A1. Mutation of a single arginine reduced the depurination activity of Stx1A1 more than that of Stx2A1. In contrast, mutation of at least two arginines was necessary to reduce depurination by Stx2A1 to a level similar to that of Stx1A1. R176A and R172A/R176A mutations eliminated interaction of Stx1A1 and Stx2A1 with ribosomes and with the stalk, while mutation of Arg170 at the active site reduced the binding affinity of Stx1A1 and Stx2A1 for the ribosome, but not for the stalk. These results demonstrate that conserved arginines at the distal face of the active site are critical for interactions of Stx1A1 and Stx2A1 with the stalk, while a conserved arginine at the active site is critical for non-stalk-specific interactions with the ribosome. Arginine mutations at either site reduced ribosome interactions of Stx1A1 and Stx2A1 similarly, indicating that conserved arginines are critical for ribosome interactions but do not contribute to the higher affinity of Stx2A1 for the ribosome.
Emotional well‐being does not predict survival in head and neck cancer patients (2008)

In their recent article, Coyne et al.1 vastly overstated the quality of their study and the meaning of their findings. They used only 4 items from an Emotional Well-Being subscale, which hardly constitutes a reliable assessment of depression or anything else, and produces little variance. Coyne et al stated that the subscale contains 5 items,1 but it actually contains 6.2 Furthermore, the questions utilized do not assess how the person handles their distress (eg, by avoidance, suppression of emotion, substance abuse, etc.).3 Moreover, although the patients in the study had squamous cell carcinomas, the validation was performed on a sample of 240 breast cancer patients. Reliability and validity are population specific. Approximately 38% of the sample did not complete the Functional Assessment of Cancer Therapy: General (FACT-G) at baseline. They were sicker (poorer Karnofsky scores) and were likely to have a poorer quality of life and more depression. Sample bias further restricted the range of response in both mood and survival. Within Radiation Therapy Oncology Group (RTOG) 9003, subjects were randomized to 4 treatments, and within RTOG 9111, they were randomized to 3 treatments. Hence, there were 7 different treatments, which differentially affected survival. It is invalid simply to perform Kaplan-Meier comparisons muddling all the subjects in the 7 strata. Furthermore, including any variable that is correlated with the FACT-G in the model removes some of the FACT-G effect before it is examined. Thus, the analyses reported are not valid and that, coupled with poor measurement and poor analytic choices, may explain the inability of the study to detect any effects. Coyne et al.1 confound hypotheses regarding whether psychotherapeutic interventions promote survival, and the idea that baseline emotional well-being is predictive of survival. Absence of proof is not proof of absence. Finding no statistical significance on a test of a hypothesis does not prove the null hypothesis. Furthermore, the authors make a point of criticizing studies linking psychosocial support with longer cancer survival that did not have an a priori hypothesis to that effect. It is inconceivable that the data in this study were collected with the a priori hypothesis that 4 of 27 questions on the FACT-G would predict shorter survival. It would appear that Coyne et al were data dredging in a biased subsample using an inadequate measure and the wrong analyses, and found nothing. That is hardly surprising, and it proves nothing. David Spiegel MD*, Helena C. Kraemer PhD*, * Department of Psychiatry and Behavioral Sciences, Stanford University Medical Center, Stanford, California.
Multi-layer video broadcasting with low channel switching delays (2009)

Modern mobile devices, despite their small sizes, can run many multimedia applications that were only possible to stationary workstations. Mobile devices, however, have quite heterogeneous resources, which poses a challenge to mobile TV broadcast networks. We study the problem of broadcasting multi-layer video streams to mobile devices with heterogeneous resources. We propose broadcast schemes that allow each mobile device to selectively receive a few (or all) layers of the complete video streams, and achieve proportional energy saving. We also propose a broadcast scheme that achieves low channel switching delay, which is important to user experience. We analytically analyze the performance of the proposed schemes. Most importantly, we have implemented them in a real mobile TV testbed. We conduct extensive experiments to show the practicality and efficiency of the proposed schemes. The experimental results show that channel switching delays less than 200 msec and energy saving between 75% and 95% are possible under typical system parameters of mobile TV networks.
Ultrasound-Targeted Microbubble Destruction Can Repeatedly Direct Highly Specific Plasmid Expression to the Heart (2003)

Ultrasound-mediated destruction of microbubbles directs plasmid transgene expression to the heart with much greater specificity than viral vectors and can be regulated by repeated treatments. This noninvasive technique is a promising method for cardiac gene therapy.
Rerouting the Plant Phenylpropanoid Pathway by Expression of a Novel Bacterial Enoyl-CoA Hydratase/Lyase Enzyme Function (2001)

The gene for a bacterial enoyl-CoA hydratase (crotonase) homolog (HCHL) previously shown to convert 4-coumaroyl-CoA, caffeoyl-CoA, and feruloyl-CoA to the corresponding hydroxybenzaldehydes in vitro provided an opportunity to subvert the plant phenylpropanoid pathway and channel carbon flux through 4-hydroxybenzaldehyde and the important flavor compound 4-hydroxy-3-methoxybenzaldehyde (vanillin). Expression of the Pseudomonas fluorescens AN103 HCHL gene in two generations of tobacco plants caused the development of phenotypic abnormalities, including stunting, interveinal chlorosis and senescence, curled leaf margins, low pollen production, and male sterility. In second generation progeny, the phenotype segregated with the transgene and transgenic siblings exhibited orange/red coloration of the vascular ring, distorted cells in the xylem and phloem bundles, and lignin modification/reduction. There was depletion of the principal phenolics concomitant with massive accumulation of novel metabolites, including the glucosides and glucose esters of 4-hydroxybenzoic acid and vanillic acid and the glucosides of 4-hydroxybenzyl alcohol and vanillyl alcohol. HCHL plants exhibited increased accumulation of transcripts for phenylalanine ammonia-lyase, cinnamate-4-hydroxylase, and 4-coumarate:CoA ligase, whereas beta-1,3-glucanase was suppressed. This study, exploiting the ability of a bacterial gene to divert plant secondary metabolism, provides insight into how plants modify inappropriately accumulated metabolites and reveals the consequences of depleting the major phenolic pools.
Induction of Cytotoxic CD8 + CD56 + T Cells from Human Thymocytes by Interleukin-15 (2001)

CD8(+) CD56(+) cells isolated from human peripheral blood lymphocytes have been shown recently to represent a population of cytotoxic active T cells. However, it is not known if these cells are intrathymically or extrathymically developed or how these cells are influenced by growth factors. In the present study, we investigated the effects of interleukin-2 (IL-2) and IL-15 on human thymocytes with respect to development of CD8(+) CD56(+) T cells. Freshly isolated thymocytes contain few CD8(+) CD56(+) cells, but the number of these cells increases significantly when thymocytes are grown in the presence of IL-15 or IL-2. However, IL-15 induced a significantly higher fraction of CD8(+) CD56(+) cells compared with IL-2. Thus, although IL-2 and IL-15 are known to have a number of redundant functions, we here demonstrate that IL-15 is superior to IL-2 in inducing CD8(+) CD56(+) T cells from cultures of thymocytes. The majority of the IL-15-grown CD8(+) CD56(+) cells were CD45R0(+), representing a memory phenotype, and showed high expression of the IL-15R-complex and high numbers of CD69(+) cells. Moreover, cytotoxic activity was confined to this cell population.
Low-Complexity Wake-up Detector for underwater acoustic MODEM (2019)

Underwater acoustic MODEMs are usually powered by batteries, it is very important to design a low-power wake-up detector to save the power of modems. This paper proposes a low-complexity wake-up detector for underwater acoustic MODEM. A balanced Gold sequence is used to design a two-phase code signal as the wake-up signal. A detector algorithm is proposed that requires only one addition, one subtraction and two multiplication operations for each sample, thus achieving low computational complexity, at the same time, the algorithm can also provide accurate Doppler estimation and rough arrival time estimation for the wake-up signal. The proposed wake-up detection algorithm has been successfully tested in the lake experiment, the results show that, the proposed detector achieves high detection rate and low false alarm rate. Therefore it is suitable as a low-power wake-up detector for underwater acoustic MODEM.