gebhart/patrepeval huggingface dataset:
p-Nitrophenyl 3-diazopyruvate and diazopyruvamides, a new family of photoactivatable cross-linking bioprobes (1989)

p-Nitrophenyl 3-diazopyruvate (DAPpNP) has been developed as a heterobifunctional cross-linking agent for synthesis of photoaffinity probes and photoactivatable cross-linking agents that are nucleophile specific. p-Nitrophenyl chloroglyoxylate is formed in high yield from oxalyl chloride and p-nitrophenol. Subsequent reaction with diazomethane produces DAPpNP in 50-60% overall yield. DAPpNP acylates primary and secondary amines to form 3-diazopyruvamides in high yields. 3-Diazopyruvamide derivatives have been formed from a wide variety of amines including aromatic amines, amino acids, and peptides. 3-Diazopyruvamides undergo photolysis and Wolff rearrangement at 300 nm to produce a ketene amide, which efficiently acylates nucleophilic species to form malonic acid amide derivatives. A family of photoactivatable 3-diazopyruvamide cross-linking agents was synthesized from amino acids. A cleavable, thiol-specific photoactivatable cross-linking agent was synthesized from cystamine. These reagents were caused to react with rabbit muscle aldolase to form mainly dimeric cross-linked species.
Gemini-Induced Columnar Jointing in Vitreous Ice. Cryo-HRSEM as a Tool for Discovering New Colloidal Morphologies (2002)

A gemini surfactant is able to promote columnar jointing in vitreous ice where long pillars, often of hexagonal cross section, are formed. This jointing is visible by cryo-high-resolution scanning electron microscopy (cryo-HRSEM), in which colloidal suspensions in bulk water are cooled rapidly in liquid ethane, thereby avoiding the potential artifacts with other types of EM. The jointing is proposed to arise from a new type of colloidal morphology where the surfactant self-assembles into hexagonal columns. Evidence for this mechanism comes from a cryo-HRSEM photo of an ice-free hexagonal "skeleton" composed of surfactant. Cryo-HRSEM, a method that is just beginning to realize its potential, would seem to have a promising future in the discovery of additional and as yet unimagined colloidal structures.
Enterprise wrappers for information assurance (2004)

Network Associates Laboratories research focused on three fundamental challenges for practically deploying non-bypassable system-call and library-call wrappers across an enterprise: 1) how to securely manage multi-platform, multi-vendor wrapper configurations over a network, 2) how to manage data flow, using both "push" and "pull" models, to facilitate intelligent, network-wide detection and response capabilities, and 3) how to write wrappers that take advantage of their new, networked environment without burdening the wrapper writer with system- and network-specific details. To meet these challenges, we: 1) identified extensions to our Wrapper Definition Language (WDL), database, and Wrapper Query Language (WQL) to permit high-level, abstract interactions with networked components, 2) developed policy specification, built a technology base, created APIs for host and network controllers, developed a new GUI, updated the wrappers, and demonstrated the new policy function, and 3) developed a boundary controller and other cross-platform components for interoperability. The results provide an architecture and prototype implementation for enforcing security policies at system-call and library-call levels across platforms and throughout an enterprise.
The Development of a Social Networking–Based Relatedness Intervention Among Young, First-Time Blood Donors: Pilot Study (2018)

ClinicalTrials.gov NCT02717338; https://clinicaltrials.gov/ct2/show/NCT02717338 (Archived by WebCite at http://www.webcitation.org/6ymHRBCwu)
AAV-Mediated Artificial miRNA Reduces Pathogenic Polyglucosan Bodies and Neuroinflammation in Adult Polyglucosan Body and Lafora Disease Mouse Models (2022)

Adult polyglucosan body disease (APBD) and Lafora disease (LD) are autosomal recessive glycogen storage neurological disorders. APBD is caused by mutations in the glycogen branching enzyme (GBE1) gene and is characterized by progressive upper and lower motor neuron dysfunction and premature death. LD is a fatal progressive myoclonus epilepsy caused by loss of function mutations in the EPM2A or EPM2B gene. These clinically distinct neurogenetic diseases share a common pathology. This consists of time-dependent formation, precipitation, and accumulation of an abnormal form of glycogen (polyglucosan) into gradually enlarging inclusions, polyglucosan bodies (PBs) in ever-increasing numbers of neurons and astrocytes. The growth and spread of PBs are followed by astrogliosis, microgliosis, and neurodegeneration. The key defect in polyglucosans is that their glucan branches are longer than those of normal glycogen, which prevents them from remaining in solution. Since the lengths of glycogen branches are determined by the enzyme glycogen synthase, we hypothesized that downregulating this enzyme could prevent or hinder the generation of the pathogenic PBs. Here, we pursued an adeno-associated virus vector (AAV) mediated RNA-interference (RNAi) strategy. This approach resulted in approximately 15% reduction of glycogen synthase mRNA and an approximately 40% reduction of PBs across the brain in the APBD and both LD mouse models. This was accompanied by improvements in early neuroinflammatory markers of disease. This work represents proof of principle toward developing a single lifetime dose therapy for two fatal neurological diseases: APBD and LD. The approach is likely applicable to other severe and common diseases of glycogen storage.
SEL1L and Squamous Cell Carcinoma of the Esophagus (2004)

The gene SEL1L is involved both in human breast and pancreatic cancer progression. It is located on 14q24.3-31, a region known to be lost in invasive cancer of the esophagus. We aimed to assess whether SEL1L could become a useful biomarker for this cancer. We assessed SEL1L mRNA and protein expression in 35 patients and found it to be weak in low-grade and strong in high-grade dysplasia. Although the majority of cancer patients showed differential expression (mRNA and protein) of SEL1L, in five cases it was completely absent; these patients had the worst outcomes. SEL1L immunoreactivity was negative in normal tissue samples from five patients with mild esophagitis as well as in normal mucosa adjacent to the tumor. We hypothesize that SEL1L could influence those cellular changes that mediate the transition from a normal mucosa to a neoplastic lesion and may help in the identification of those patients at higher risk of developing this cancer. The specific impact of SEL1L in esophageal cancer needs further investigation.
Answer to last month's radiology case and image: Bilateral patellar tendon rupture. (2009)

Patellar tendon rupture is a rare occurrence usually associated with chronic degeneration within the tendon, systemic illness, and fluoroquinolone therapy as mentioned previously. However in healthy adults, overweight men in their 3rd or 4th decade of life may be at increased risk when partaking in athletic activities, especially jumping activities. Patella alta is a key finding on physical exam and on radiographs as was evident in our case. Imaging can also be performed with ultrasound and MRI to confirm tendon rupture and rule out other concurrent injuries. Prompt surgical management and early rehabilitation are key to regaining normal function of the extensor mechanism. Preventive medicine education may be important for those at increased risk of injury.
Characterization of a Unique Nonsecretory Ribonuclease from Urine of Pregnant Women1 (1992)

We have reported previously [Sakakibara, et al. (1991) Chem. Pharm. Bull. 39, 146-149] that a protein purified from a partially purified pharmaceutical preparation of human chorionic gonadotropin (a urinary protein preparation from pregnant women) is a unique nonsecretory ribonuclease (RNase)-like protein on the basis of its amino terminal sequence homology. We purified the protein further from the same materials by gel filtration and reversed-phase column chromatographies with RNase activity as an index. The purified protein was designated RNase UpI-2. The catalytic activity and its sensitivity to inhibition by divalent cations suggest that the protein is related to nonsecretory RNase. The estimated molecular weight of RNase UpI-2 (38 kDa) by sodium dodecyl sulfate-polyacrylamide gel electrophoresis was significantly higher than that of urinary nonsecretory RNases (13 to 19 kDa) reported so far. After trifluoromethanesulfonic acid treatment, the molecular weight of RNase UpI-2 was reduced and approached that of nonsecretory RNase, which indicated that the protein contains a significant amount of carbohydrate (approximately 50%). RNase UpI-2 was immunoreactive with antibodies to a nonsecretory RNase, RNAase 1 [Yasuda et al. (1988) Biochim. Biophys. Acta 965, 185-194]. By immunoblot analysis of the protein freshly prepared from various urine samples, it was shown that a considerable amount of RNase UpI-2 is present in urine of pregnant women, but only a trace of RNase UpI-2, if any, was detected in urine of nonpregnant women and men. These results suggest the possibility that RNase UpI-2 may have been formed via a specific protein modification in pregnant women.
Extracorporeal immunoadsorption with protein A: Technical aspects and clinical results (2001)

Abstract The use of therapeutic plasma exchange (TPE) for removal of large molecular‐weight substances form patients' circulation is limited by the method's non‐selectivity and non‐specificity. In order to remove the target amount of pathogenic substance, usually amounting to less than 1 g per liter of plasma, one will also remove 60‐80 g of proteins, some of which are essential. A further disadvantage of the method is the need for substitution fluids, which at least in some countries are expensive and of limited availability. Furthermore, there is a (low) risk of disease transmission. To overcome these limitations, the principle of affinity chromatography used in biochemistry was applied in medicine to develop the Excorim Extracorporeal Immunoadsorption System in the beginning of the 1980s [1].
Morphometric analysis of skeletal muscle growth in the high growth mouse. (1994)

The high growth phenotype in the mouse results from a single autosomal recessive locus (hg) mapped to chromosome 10, that produces a marked increase in growth rate and body size compared to controls. Using morphometric methods, we quantified skeletal muscle growth in newborn male and female high growth mice, and at 3, 6, and 9 weeks of age. Adult male high growth mouse body weights increased by 42% and muscle weights increased 39-43% compared to controls. Differences between high growth and control muscle weights were removed after normalization to body weight. Similar changes in muscle and body weights were found in female high growth mice. Muscle cross-sectional area was significantly (P < 0.05) increased in high growth mouse gastrocnemius (GAS), soleus (SOL), and tibialis anterior (TA) muscles at 6 and 9 weeks of age. Cross-sectional areas of slow type 1, and fast type 2b fibers were moderately increased in all high growth muscles measured. Muscle fiber number was increased by approx 30% in the high growth SOL, GAS and TA muscles. We conclude that rapid growth in the high growth mouse is accompanied by an increase in muscle mass, due to fiber hyperplasia and hypertrophy, and that the hg locus may act during myogenesis to alter the proliferation rate and/or fusion kinetics of high growth mouse muscle cells.
Role of MbtH-like Proteins in the Adenylation of Tyrosine during Aminocoumarin and Vancomycin Biosynthesis (2011)

MbtH-like proteins consist of ∼70 amino acids and are encoded in the biosynthetic gene clusters of non-ribosomally formed peptides and other secondary metabolites derived from amino acids. Recently, several MbtH-like proteins have been shown to be required for the adenylation of amino acid in non-ribosomal peptide synthesis. We now investigated the role of MbtH-like proteins in the biosynthesis of the aminocoumarin antibiotics novobiocin, clorobiocin, and simocyclinone D8 and of the glycopeptide antibiotic vancomycin. The tyrosine-adenylating enzymes CloH, SimH, and Pcza361.18, involved in the biosynthesis of clorobiocin, simocyclinone D8, and vancomycin, respectively, required the presence of MbtH-like proteins in a 1:1 molar ratio, forming heterotetrameric complexes. In contrast, NovH, involved in novobiocin biosynthesis, showed activity in the absence of MbtH-like proteins. Comparison of the active centers of CloH and NovH showed only one amino acid to be different, i.e. Leu-383 versus Met-383. Mutation of this amino acid in CloH (L383M) indeed led to MbtH-independent adenylating activity. All investigated tyrosine-adenylating enzymes exhibited remarkable promiscuity for MbtH-like proteins from different pathways and organisms. YbdZ, the MbtH-like protein from the expression host Escherichia coli, was found to bind to adenylating enzymes during expression and to influence their biochemical properties markedly. Therefore, the use of ybdZ-deficient expression hosts is important in biochemical studies of adenylating enzymes.
Formulating Industry-Academic Collaborations That Work: Best Practices to Ensure A Strong Relationship After the Agreements are Signed (2020)

Collaborations between academia and industry are growing in scope, duration, and sophistication. The best collaborations recognize the unique strengths and skill sets of both parties and are structured to leverage what each party does best. In many cases, these collaborations develop into long-term relationships, and it is important to develop the systems and structures needed to support these relationships to ensure that they meet the needs of both sides. Successful collaborations require the formulation of a governance structure to facilitate communication, decision-making, assessment of progress, and the inevitable changes of direction that accompany product development. This panel explored the pragmatic aspects of successfully structuring collaborations and managing the relationships after the deal is done. Several dominant themes associated with successful collaborative relationships emerged from the discussion, and these will be explored in this article.
Memory size bounds of prefix DAGs (2013)

In this report an entropy bound on the memory size is given for a compression method of leaf-labeled trees. The compression converts the tree into a Directed Acyclic Graph (DAG) by merging isomorphic subtrees.
Distinctive immunoregulatory effects of adenosine on T cells of older humans (2011)

A role for adenosine in immunosenescence was investigated in T cells from older (≥65 yr) and younger (24-45 yr) healthy humans. Adenosine concentrations in cultures of activated T cells were significantly higher (P<0.0001) for older (145±47 nM, mean±sd) than younger (58±5.5 nM) subjects. Expression of the activation coreceptor CD28 was suppressed significantly by 0.1 to 1 μM exogenous adenosine, with greater effects of 1 μM (P<0.01) on T cells of younger (mean suppression of 67 and 65% for CD4 and CD8 T cells, respectively) than older (means of 42 and 46%) subjects. T-cell chemotaxis to CCL21 was suppressed significantly by 0.3 and 1 μM exogenous adenosine, with mean maximum decreases of 39 and 49%, respectively, for younger subjects and 28 and 31% for older subjects. Generation of IL-2 and IFN-γ by T cells of younger and older subjects was suppressed substantially only at adenosine levels of 3 μM or higher. Lower baseline expression of CD28 and chemotaxis to CCL21 and S1P for T cells from older subjects attributable to endogenous adenosine were reversed completely by two different A(2A) adenosine receptor antagonists without affecting T cells of younger subjects. Adenosine is an endogenous T-cell immunosuppressor in older humans, and A(2A) antagonists reverse adenosine-induced T-cell deficiencies of aging.
Film Side Laser Patterning of Molybdenum Thin Films Sputter-Deposited onto Glass (2012)

Serial interconnection of CIGSe thin film solar modules involves typically glass-side laser patterning of the molybdenum layer (P1 scribe). In this paper we present a working principle of P1 film side patterning. The investigated samples were sputter-deposited onto soda-lime glass substrates. For understanding the fundamental ablation behavior, two kinds of layer systems were studied: on the one hand monolayer systems which are compressively stressed and on the other hand bilayer systems, consisting of a tensile stressed layer on the substrate and a second layer on top. The film-side ablation process was studied using a nanosecond as well as a picosecond laser source. The influence of intrinsic stress was studied by XRD. Time resolved spectroscopy reveals the formation of plasma as important driving mechanism for ablation. It is shown that by proper adaption of the sputter conditions high-quality P1 film side patterning is achieved.
Integrated dry NO{sub x}/SO{sub 2} emissions control systems: Advanced retractable injection lance SNCR test report. NOELL ARIL test period: April 20, 1995--December 21, 1995; DPSC test period: August 16--26, 1996 (1997)

The test site is Arapahoe Generating Station Unit 4, a 100 MWe down-fired utility boiler burning a low-sulfur western coal. The project goal is to demonstrate up to 70% reductions in NOx and SO{sub 2} emission through the integration of: (1) down-fired low-NOx burners with overfire air; (2) Selective Non-Catalytic Reduction (SNCR) for additional NOx removal; and (3) dry sorbent injection and duct humidification for SO{sub 2} removal. This report documents the third phase of SNCR tests, where an additional injection location was installed to increase the low-load NOx removal performance. The new injectors consist of a pair of retractable in-furnace lances which were designed to provide a high degree of load following flexibility through on-line adjustments of the injection angle. With the new lances, NOx removals in excess of 35% are achievable at the same load and HN{sub 3} slip limit. At loads of 43 to 60 MWe, NOx removals with the lances range from 37--52%. At loads greater than 60 MWe, the wall-injection location is more efficient, and at loads of 70 to 100 MWe, NOx removals range from 37--41%. The coal mill-in-service pattern was found to have a large effect on both NOx removal and NH{sub 3} slip for injection at the new lance location. At 60 MWe, the NOx removal at the 10 ppm NH{sub 3} slip limit ranges from 28--52% depending on the mill-in-service pattern. Biasing the coal mills to provide uniform combustion conditions ahead of the injection location was found to be the best option for improving SNCR system performance under these conditions.
Accuracy of Elastic Fusion of Prostate Magnetic Resonance and Transrectal Ultrasound Images under Routine Conditions: A Prospective Multi-Operator Study (2016)

Registration error values were reasonable for clinical practice. The co-registration accuracy was significantly influenced by the operator's experience, and significantly poorer in the antero-posterior direction and at the apex.
Intradialytic Central Venous Oxygen Saturation is Associated with Clinical Outcomes in Hemodialysis Patients (2017)

Central venous oxygen saturation (ScvO<sub>2</sub>) in the superior vena cava is predominantly determined by cardiac output, arterial oxygen content, and oxygen consumption by the upper body. While abnormal ScvO<sub>2</sub> levels are associated with morbidity and mortality in non-uremic populations, ScvO<sub>2</sub> has received little attention in hemodialysis patients. From 1/2012 to 8/2015, 232 chronic hemodialysis patients with central venous catheters as vascular access had their ScvO<sub>2</sub> monitored during a 6-month baseline period and followed for up to 36 months. Patients were stratified into upper and lower two tertiles by a ScvO<sub>2</sub> of 61.1%. Survival analysis employed Kaplan-Meier curves and adjusted Cox proportional hazards models. Patients in the lower tertiles of ScvO<sub>2</sub> were older, had longer hemodialysis vintage, lower systolic blood pressure, lower ultrafiltration rates, higher leukocyte counts and neutrophil-to-lymphocyte ratios. Kaplan-Meier analysis indicated a shorter survival time in the lower tertiles of ScvO<sub>2</sub> (P = 0.005, log-rank test). In adjusted Cox analysis, a 1 percent point decrease in mean ScvO<sub>2</sub> was associated with a 4% increase in mortality (HR 1.04 [95% CI 1.01-1.08], P = 0.044), indicating that low﻿ ScvO<sub>2</sub> is associated with poor outcomes. Research on the relative contributions of cardiac output and other factors is warranted to further elucidate the pathophysiology underlying this novel finding.
Effects of an over-the-counter lactic-acid containing intra-vaginal douching product on the vaginal microbiota (2019)

The Etos® douche did not significantly affect the vaginal pH or VM composition, although increased odds for having diverse anaerobic VM was observed, especially when douching during menses. Furthermore, douching may promote C. albicans infections.
Inhibition of Mast Cell–Dependent Conversion of Cultured Macrophages Into Foam Cells With Antiallergic Drugs (2000)

Degranulation of isolated, rat peritoneal mast cells in the presence of low density lipoprotein (LDL) induces cholesteryl ester accumulation in cocultured macrophages with ensuing foam cell formation. This event occurs when the macrophages phagocytose LDL particles that have been bound to the heparin proteoglycans of exocytosed granules. In an attempt to inhibit such foam cell formation pharmacologically, rat peritoneal mast cells that had been passively sensitized with anti-ovalbumin-IgE were treated with 2 mast cell-stabilizing antianaphylactic drugs, MY-1250 or disodium cromoglycate (DSCG). Both drugs were found to inhibit antigen (ovalbumin)-triggered release of histamine from the mast cells, revealing mast cell stabilization. In cocultures of rat peritoneal macrophages and passively sensitized mast cells, addition of MY-1250 before addition of the antigen resulted in parallel reductions in histamine release from mast cells, uptake of [(14)C]sucrose-LDL, and accumulation of LDL-derived cholesteryl esters in the cocultured macrophages. Similarly, when passively sensitized mast cells were stimulated with antigen in the presence of DSCG and the preconditioned media containing all substances released from the drug-treated mast cells were collected and added to macrophages cultured in LDL-containing medium, uptake and esterification of LDL cholesterol by the macrophages were inhibited. The inhibitory effects of both drugs were mast cell-specific because neither drug inhibited the ability of macrophages to take up and esterify LDL cholesterol. Analysis of heparin proteoglycan contents of the incubation media revealed that both drugs had inhibited mast cells from expelling their granule remnants. Thus, both MY-1250 and DSCG prevent mast cells from releasing the heparin proteoglycan-containing vehicles that bind LDL and carry it into macrophages. This study suggests that antiallergic pharmacological agents could be used in animal models to prevent mast cell-dependent formation of foam cells in vivo.
Three-Dimensional Surface Displacements From InSAR and GPS Measurements With Variance Component Estimation (2012)

Previous approaches that integrate interferometric synthetic aperture radar (InSAR) and GPS measurements for 3-D surface displacement mapping require statistically estimating the variances of the measurements to yield optimal results. We present a variance component estimation approach to weigh the InSAR and GPS measurements in deriving 3-D surface displacements. The approach exploits the observations themselves for determining the weighting scheme, and therefore the a priori information on the stochastic model of the observations is not required. This is of great importance as accurate knowledge on the stochastic model is often unavailable. The performance of the proposed method is validated with both simulated and real datasets.