gebhart/patrepeval huggingface dataset:
Evaluation of a Mixed Meal Test for Diagnosis and Characterization of PancrEaTogEniC DiabeTes Secondary to Pancreatic Cancer and Chronic Pancreatitis (2018)

Pancreatogenic diabetes mellitus is most commonly the result of chronic pancreatitis but can also occur secondary to pancreatic cancer. The early identification of pancreatogenic diabetes and distinction from the more prevalent type 2 diabetes are clinically significant; however, currently, there is no validated method to differentiate these diabetes subtypes. We describe a study, "Evaluation of a Mixed Meal Test for Diagnosis and Characterization of PancrEaTogEniC DiabeTes Secondary to Pancreatic Cancer and Chronic Pancreatitis: the DETECT study," that seeks to address this knowledge gap. The DETECT study is a multicenter study that will examine differences in hormone and glucose excursions after a mixed meal test. The study will also create a biorepository that will be used to evaluate novel diagnostic biomarkers for differentiating these diabetes subtypes.
Acute renal failure in patients with sepsis (2007)

The evaluation of acute renal failure (ARF) by the newly developed classification for ARF (RIFLE, standing for 'risk, injury, failure, loss, end-stage kidney disease') [1] in patients with sepsis has not yet been performed. We evaluated, retrospectively, the incidence of ARF and its risk factors, therapy, and outcome among patients with sepsis admitted to the Infectious Diseases Intensive Care Unit of the Hospital de Santa Maria between January 2005 and December 2006. ARF was defined by means of the RIFLE classification [1]. Sepsis was classified in accordance with the American College of Chest Physicians and the Society of Critical Care Medicine consensus [2]. In all, 182 patients (aged 56.2 ± 18.56 years (mean ± SD), 120 male, 162 Caucasian) were analyzed. Baseline characteristics of the patients are summarized in Table ​Table1.1. Sixty-eight patients (37.4%) had ARF. By multivariate analysis, age more than 60 years (odds ratio (OR) 0.39, 95% confidence interval (CI) 0.17 to 0.87, P = 0.002), male (OR 5.5, 95% CI 2.2 to 13.5, P 50 (OR 0.14, 95% CI 0.06 to 0.31, P 50, comorbidity (namely cardiovascular disease), and ARF showed that SAPS II > 50 (OR 0.12, 95% CI 0.05 to 0.29, P < 0.0001) and ARF (OR 0.26, 95% CI 0.11 to 0.63, P = 0.003) were independent predictors of mortality.



Table 1

Baseline characteristics



Thus, ARF as determined by RIFLE is common among patients with sepsis, and increases mortality. Age, gender, chronic kidney disease, Gram-negative-related infection and severity of illness are independently associated with ARF in this setting.
Dysregulation of RNA Splicing in Tauopathies (2019)

Pathological aggregation of RNA binding proteins (RBPs) is associated with dysregulation of RNA splicing in PS19 P301S tau transgenic mice and in Alzheimer's disease brain tissues. The dysregulated splicing particularly affects genes involved in synaptic transmission. The effects of neuroprotective TIA1 reduction on PS19 mice are also examined. TIA1 reduction reduces disease-linked alternative splicing events for the major synaptic mRNA transcripts examined, suggesting that normalization of RBP functions is associated with the neuroprotection. Use of the NetDecoder informatics algorithm identifies key upstream biological targets, including MYC and EGFR, underlying the transcriptional and splicing changes in the protected compared to tauopathy mice. Pharmacological inhibition of MYC and EGFR activity in neuronal cultures tau recapitulates the neuroprotective effects of TIA1 reduction. These results demonstrate that dysfunction of RBPs and RNA splicing processes are major elements of the pathophysiology of tauopathies, as well as potential therapeutic targets for tauopathies.
Field Applications of Low Molecular-Weight Polymer Activated with an Organic Crosslinker for Water Conformance in South Mexico (2004)

Abstract One of the major challenges faced in the Mexico South region is water management. Water in the oil stream results in extra disposal costs, scale buildup, reduced oil production, and eventually well shut-in (with associated workover costs). Consequently, producing zones are often abandoned in an attempt to avoid water contact, even when the intervals still retain large volumes of recoverable hydrocarbons. Although natural fractures have a positive effect on oil flow, they also include a negative water or gas flow caused by coning effects or conductive streaks between the producing hydrocarbon zone and intervals above or below. If these zones are water producers, they soon impact the productivity of the hydrocarbon zone. An additional problem must be addressed as well: early water breakthrough caused by edge water flowing through faults, natural fractures, etc. Depending on the desired objective, placement techniques vary. However, placement techniques generally can be divided into two types: those involving a workover rig and those that are rig-less. This paper will discuss case histories from southern Mexico that have used a low molecular-weight polymer, activated with an organic crosslinker. The candidate selection process, general job designs, laboratory testing results, etc. performed for water-reduction treatments in this area will be presented. These cases include depleted, highly fractured reservoirs.
ChemInform Abstract: Titanium Oxo‐Clusters: Precursors for a Lego‐Like Construction of Nanostructured Hybrid Materials (2011)

Abstract Review: 137 refs.
Supplementary figure legends from CD47 Enhances <i>In Vivo</i> Functionality of Artificial Antigen-Presenting Cells (2023)

&lt;p&gt;Supplementary figure legends&lt;/p&gt;
Targeted complement inhibition at synapses prevents microglial synaptic engulfment and synapse loss in demyelinating disease (2019)

Summary Multiple sclerosis (MS) is a demyelinating, autoimmune disease of the central nervous system. While work has focused on axon loss in MS, far less is known about synaptic changes. Here, in striking similarity to other neurodegenerative diseases, we identify in postmortem human MS tissue and in nonhuman primate and mouse MS models profound synapse loss and microglial synaptic engulfment. These events can occur independently of local demyelination, neuronal degeneration, and peripheral immune cell infiltration, but coincide with gliosis and increased localization of complement component C3, but not C1q, at synapses. Finally, we use AAV9 to overexpress the complement inhibitor Crry at activated C3-bound synapses in mice and demonstrate robust protection of synapses and visual function. These results mechanistically dissect synapse loss as an early pathology in MS. We further provide a novel gene therapy approach to prevent synapse loss by microglia, which may be broadly applicable to other neurodegenerative diseases.
Signaling pathways that regulate blood vessel morphogenesis (2006)

We study how signals are integrated to regulate morphogenetic processes during blood vessel formation, and how cell division and morphogenesis are co‐ordinated. We utilize a stem cell model that allows for in vitro formation of blood vessels via vasculogenesis and angiogenic sprouting. We have incorporated GFP reporters into the developing vessels for dynamic imaging. Using these reagents, we have studied the role of the VEGF receptor flt‐1 (VEGFR‐1) in vessel morphogenesis using cells lacking flt‐1. Our data shows that flt‐1 normally negatively regulates endothelial cell division, but it positively regulates sprouting morphogenesis. This occurs primarily through the activity of a soluble form of the receptor (sflt‐1), as rescue with this isoform is more efficient than rescue with membrane‐localized isoforms. We also investigate the role of a Ras/Rap activator called RasGRP3. RasGRP3 is a novel endothelial DAG/phorbol ester receptor that mediates a florid dysmorphogenesis upon treatment of embryonic vessels with phorbol esters. The pathway downstream of RasGRP3 resembles a pathway that leads to vessel permeability. Thus we hypothesize that RasGRP3, which is not required for viability, is important in pathological situations to regulate permeability. RasGRP3 expression is regulated by VEGF, and we are currently investigating whether it is functionally downstream of effects of VEGF on morphogenesis and permeability.
Anionic phospholipids control mechanisms of GPCR-G protein recognition (2023)

G protein-coupled receptors (GPCRs) are embedded in phospholipids that strongly influence drug-stimulated signaling. Anionic lipids are particularly important for GPCR signaling complex formation, but a mechanism for this role is not understood. Using NMR spectroscopy, we explore the impact of anionic lipids on the function-related conformational equilibria of the human A<sub>2A</sub> adenosine receptor (A<sub>2A</sub>AR) in bilayers containing defined mixtures of zwitterionic and anionic phospholipids. Anionic lipids prime the receptor to form complexes with G proteins through a conformational selection process. Without anionic lipids, signaling complex formation proceeds through a less favorable induced fit mechanism. In computational models, anionic lipids mimic interactions between a G protein and positively charged residues in A<sub>2A</sub>AR at the receptor intracellular surface, stabilizing a pre-activated receptor conformation. Replacing these residues strikingly alters the receptor response to anionic lipids in experiments. High sequence conservation of the same residues among all GPCRs supports a general role for lipid-receptor charge complementarity in signaling.
Defining a common region of deletion at 13q21 in human cancers (2001)

Previous molecular genetic analyses identified a region of deletion at 13q21 in a variety of human cancers, suggesting the existence of a tumor suppressor gene(s) at this locus. In our earlier study on prostate cancer, the region of deletion was confined to a 3.1 cM interval between D13S152 and D13S162. At present, however, no known gene located in this interval has been firmly implicated in cancer, and the region remains too large for gene identification. To fine-map the area of interest, we established a contig of bacterial artificial chromosome (BAC) clones, narrowed the region of deletion by loss of heterozygosity (LOH) and homozygosity-mapping-of-deletion (HOMOD) analyses in different types of cancers, and tested a candidate gene from the region for mutation and alteration of expression in prostate cancers. The contig consisted of 75 overlapping BAC clones. In addition to the generation of 47 new sequence-tagged-site (STS) markers from the ends of BAC inserts, 76 known STS and expressed sequence tag markers were mapped to the contig (25 kb per marker on average). The minimal region of deletion was further defined to be about 700 kb between markers D13S791 and D13S166 by LOH analysis of 42 cases of prostate cancer, and by HOMOD analysis of eight prostate cancer cell lines/xenografts and 49 cell lines from cancers of the breast, ovary, endometrium, and cervix, using 18 microsatellite markers encompassing the deletion region. A gene that is homologous to the WT1 tumor suppressor gene, AP-2rep (KLF12), was mapped in this region and was analyzed for its expression and genetic mutation. In addition to low levels of expression in both normal and neoplastic cells of the prostate, this gene did not have any mutations in a group of aggressive prostate cancers and cell lines/xenografts, as assessed by the methods of polymerase chain reaction-single strand conformational polymorphism analysis and direct sequencing. These studies suggest that a 700 kb interval at 13q21 harbors a tumor suppressor gene(s) that seems to be involved in multiple types of cancer, and that the AP-2rep gene is unlikely to be an important tumor suppressor gene in prostate cancer. The BAC contig and high-resolution physical map of the defined region of deletion should facilitate the cloning of a tumor suppressor gene(s) at 13q21.
Full-Duplex Wireless Transceiver in Presence of I/Q Mismatches: Experimentation and Estimation Algorithm (2015)

In a previous work of the authors, it was shown that I/Q imbalance in the transmitter and receiver chains significantly deteriorates the achievable amount of self-interference suppression. Having there only analytically and simulatively analyzed the effect of I/Q imbalance, this paper gives experimental results and additionally extends the algorithm to also correct for the I/Q imbalance at the receiver. To avoid its degrading effect in the parameter estimation phase, the receiving chain is equipped with a tunable local oscillator (LO), allowing to receive the pilot signal at an intermediate frequency and then to digitally down-convert it. In this way, the transmitter I/Q imbalance parameters are correctly estimated. During normal operation, the LO is then set to the same frequency as the transmit chain. Experimental results show that incorporating RX I/Q imbalance increases the amount of self-interference cancellation from 45.3 dB to 53.9 dB.
Supplementary Methods, Supplementary Figures 1-8, Supplementary Tables 1-5, Supplementary References from A Gene Signature for Selecting Benefit from Hypoxia Modification of Radiotherapy for High-Risk Bladder Cancer Patients (2023)

&lt;p&gt;Table S1. Clinicopathologic details compared to original trial; Table S2. FFPE sample details by randomisation arm; Table S3 Predictive significance of the literature signatures for LPFS analysis; Table S4 Bladder cancer-specific hypoxia signature genes; Table S5. Distribution of clinicopathological factors by hypoxia signature scores; Figure S1. BCON consort diagram; Figure S2. Bladder cancer-specific hypoxia gene co-expression network; Figure S3. Fixed effect meta-analysis of the hazard ratios of the 24-gene hypoxia signature developed in this work on 6 independent cohorts; Figure S4. Distribution of 24-gene hypoxia signature score in tumours with high or low protein expressions; Figure S5. Kaplan-Meier plot for BCON patients receiving radiotherapy only; Figure S6. Kaplan-Meier plot for BCON patients having high 24-gene hypoxia signature scores and high Riester risk signature scores; Figure S7. Kaplan-Meier plot for BCON patients receiving radiotherapy only; Supplementary Figure S8. Kaplan-Meier plot for BCON patients having high 24-gene hypoxia signature scores and high Lendahl risk signature scores.&lt;/p&gt;
The Performance of Un-Instrumented In-Air Pointing (2020)

We present an analysis of in-air finger and hand controlled object pointing and selection. The study used a tracking system that required no instrumentation on the user. We compared the performance of the two pointing methods with and without elbow stabilization and found that the method that yielded the best performance varied for each participant, such that there was no method that performed significantly better than all others. We also directly compared user performance between un-instrumented inair pointing and the mouse. We found that the un-instrumented inair pointing performed significantly worse, at less than 75% of mouse throughput. Yet, the larger range of applications for un-instrumented 3D hand tracking makes this technology still an attractive option for user interfaces.123456
Report on the Aachen OCL Meeting (2014)

As a continuation of the OCL workshop during the MODELS 2013 conference in October 2013, a number of OCL experts decided to meet in November 2013 in Aachen for two days to discuss possible short term improvements of OCL for an upcoming OMG meeting and to envision possible future long-term developments of the language. This paper is a sort of \minutes of the meeting" and intended to quickly inform the OCL community about the discussion topics.
Structures of inorganic polymers in sol-gel processes based on titanium oxide (1993)

Inorganic gels and precipitates have been made through hydrolysis and condensation of the precursor Ti(${\mathrm{OBu}}^{\mathit{n}}$${)}_{4}$ dissolved in n-butanol. The condensation of uninhibited precursors leads to precipitation; the selective inhibition of condensation through ${\mathrm{H}}^{+}$ ions prevents precipitation and leads to gelation. The structures of the polymers which result from condensation in either case have been examined through small-angle x-ray scattering. It has been found that these structures vary continuously with the inhibition ratio. At high inhibition, the polymers are tenuous objects with a self-similarity exponent ${\mathit{d}}_{\mathit{f}}$\ensuremath{\approxeq}2; they invade the whole sample volume to form transparent gels. At intermediate ratios, the polymers become bushy with a self-similarity exponent ${\mathit{d}}_{\mathit{f}}$&gt;2 and they form turbid gels. Finally, precipitation occurs when ${\mathit{d}}_{\mathit{f}}$ reaches 3. These nonuniversal values of the exponents result from nonstationary growth modes, where a few large polymers grow first, and then densify through the capture of unused monomers.
Conformational equilibrium of an enzyme catalytic site in the allosteric transition (1992)

The dynamic equilibrium of a catalytic site between active and inactive conformations, the missing link between the structure and function of allosteric enzymes, was identified using protein engineering and NMR techniques. Kinetic analyses of the wild-type and three mutants of Thermus L-lactate dehydrogenase established that the allosteric property of the enzyme is associated with a concerted transition between the high-affinity (R) and low-affinity (T) states. By introducing mutations, we prepared an enzyme in which the R and T states were balanced. The conformation of the enzyme-bound coenzyme, NAD+, which interacts directly with the substrate, was analyzed using NMR spectroscopy. NAD+ bound to the mutant enzyme was in a conformational mixture of the active and inactive forms, while NAD+ took on predominantly one of the two forms when it was bound to the other enzymes we had analyzed. We interpret this to mean that the catalytic site is in equilibrium between the two conformations. The ratio of the conformers of each enzyme agreed with the [T]/[R] ratio as determined by kinetic analyses. Therefore, it is the identified conformational equilibrium of the catalytic site that governs the allosteric regulation of the enzyme activity.
Technological Journey From Colorimetric to Tandem Mass Spectrometric Measurements in the Diagnostic Investigation for Phenylketonuria (2016)

Phenylalanine analysis for phenylketonuria (PKU) detection in newborn screening (NBS) was chosen as the model system to describe how advancements in laboratory technology improved laboratory performance. These advancements have made NBS programs better and have improved the health outcomes of the affected newborn through improvements in accurate early detection over the past 50 years. The most current state-of-the-art technology, tandem mass spectrometry (MS/MS), has proven that it is now the choice in almost all modern NBS facilities because it is a versatile instrument that continues to grow in its application not just for amino acid and acylcarnitine detection but for other metabolites and disorders such as lysosomal storage diseases and second-tier detection of some screen-positive results. The use of MS/MS will continue to expand, even with the anticipated introduction and expansion of molecular screening methods into NBS programs. Regarding technological advancements, the future of NBS will include even newer technologies and approaches that will enhance the detection and treatment of newborns affected by PKU and other inborn errors of metabolism.
The role of CD200 in immunity to B cell lymphoma (2010)

CD200 is a transmembrane protein broadly expressed on a variety of cell types, which delivers immunoregulatory signals through binding to receptors (CD200Rs) expressed on monocytes/myeloid cells and T lymphocytes. Signals delivered through the CD200:CD200R axis have been shown to play an important role in the regulation of anti-tumor immunity, and overexpression of CD200 has been reported in a number of malignancies, including CLL, as well as on cancer stem cells. We investigated the effect of CD200 blockade in vitro on a generation of CTL responses against a poorly immunogenic CD200+ lymphoma cell line and fresh cells obtained from CLL patients using anti-CD200 mAb and CD200-specific siRNAs. Suppression of functional expression of CD200 augmented killing of the CD200+ cells, as well as production of the inflammatory cytokines IFN-gamma and TNF-alpha by effector PBMCs. Killing was mediated by CD8+ cytotoxic T cells, and CD4+ T cells play an important role in CD200-mediated suppression of CTL responses. Our data suggest that CD200 blockade may represent a novel approach to clinical treatment of CLL.
The Hidden cost of the Edge: A Performance Comparison of Edge and Cloud\n Latencies (2021)

Edge computing has emerged as a popular paradigm for running\nlatency-sensitive applications due to its ability to offer lower network\nlatencies to end-users. In this paper, we argue that despite its lower network\nlatency, the resource-constrained nature of the edge can result in higher\nend-to-end latency, especially at higher utilizations, when compared to cloud\ndata centers. We study this edge performance inversion problem through an\nanalytic comparison of edge and cloud latencies and analyze conditions under\nwhich the edge can yield worse performance than the cloud. To verify our\nanalytic results, we conduct a detailed experimental comparison of the edge and\nthe cloud latencies using a realistic application and real cloud workloads.\nBoth our analytical and experimental results show that even at moderate\nutilizations, the edge queuing delays can offset the benefits of lower network\nlatencies, and even result in performance inversion where running in the cloud\nwould provide superior latencies. We finally discuss practical implications of\nour results and provide insights into how application designers and service\nproviders should design edge applications and systems to avoid these pitfalls.\n
Use of Cationic Lipids to Enhance the Biological Activity of Antisense Oligonucleotides (1993)

Antisense oligonucleotides bind to specific mRNA or pre-mRNA sequences through Watson-Crick base pairing, resulting in decreased expression of the targeted protein. The use of cationic lipids to enhance cellular uptake of antisense oligonucleotides is reviewed herein. Cationic lipids such as N[1-(2,3-dioleyloxy)propyl]-N, N, N-trimethylammonium chloride (DOTMA) were found to enhance the biological activity of phosphorothioate oligonucleotides by at least 1000-fold in cell culture. Cationic lipid preparations enhanced both the rate and amount of oligonucleotide which associated with cells. In addition, DOTMA markedly changed the subcellular distribution of the oligonucleotide. In the absence of lipid, fluorescein labelled phosphorothioate oligonucleotides accumulated in discrete cytoplasmic structures. In the presence of cationic lipids, the oligonucleotides concentrated within the nucleus, were excluded from nucleoli, and localized in punctate cytoplasmic structures. The accumulation of the oligonucleotide in the nucleus was inhibited by incubation of the cells at 4°C and by monensin, but not by chloroquine, ammonium chloride, or nocodazole. Cell lines, both primary and transformed, differ markedly in their sensitivity to inhibition of gene expression with antisense oligonucleotides in the presence of cationic lipids. The differential sensitivity of the cells correlates with the amount of 35S-labelled oligonucleotide associated with the cells and the number of cells in the population which take up the oligonucleotide. Our studies have demonstrated that several types of cationic lipids markedly enhance the activity of phosphorothioate oligonucleotides in cell culture models. We are currently investigating the ability of cationic lipids to enhance activity of antisense oligonucleotides in more complex systems such as organ cultures and in animals.