gebhart/patrepeval huggingface dataset:
The College of American Pathologists Biorepository Accreditation Program: Results from the First 5 Years (2018)

The College of American Pathologists (CAP) developed the Biorepository Accreditation Program (BAP) in 2012. This program integrates best practices from the International Society for Biological and Environmental Biorepositories, the National Cancer Institute, the Organisation for Economic Cooperation and Development, the Center for Medicare and Medicaid Services, and the CAP Laboratory Accreditation Program. The goal of this elective program is to provide requirements for standardization in biorepository processes that will result in high-quality specimens that can be used to support research, drug discovery, and personalized medicine. CAP uses a peer inspection model to ensure the inspectors have proper expertise and to promote educational efforts through information sharing. Lead inspectors are comprised of pathologists, PhDs, and managers of biorepositories and they are often supported by CAP staff inspectors. Accreditation is a 3-year continuous cycle of quality with a peer inspection occurring at the start of year 1 and a self-inspection and CAP desk assessment at the start of year 2 and 3. At this time 53 biorepositories are fully CAP BAP accredited and 13 are in the process of obtaining accreditation. There are currently 273 established standards with requirement lists customized based on the scope of activities performed by a biorepository. A total of 90 inspections were completed between May 2012 and December 2016. Sixty-one were initial inspections and 29 were reinspections. A total of 527 deficiencies were identified in the areas of Equipment/Instrumentation (22%), Information Technology (18%), Specimen Handling and QC (15%), Quality Management (16%), Personnel (11%), Safety (10%), Facilities (6%), and Regulatory (2%). Assessment of common deficiencies identifies areas of focus for continuous improvement and educational opportunities. Overall success of the program is high based on the current enrollment of 66 biorepositories, anecdotal participant feedback and increasing national recognition of the BAP in federal documents.
Alkaline Pretreatment of Switchgrass (2015)

Alkaline pretreatment using sodium hydroxide offers a means to extract lignin and acetate from lignocellulosic biomass, in turn enabling higher enzymatic digestibility of the remaining polysaccharides and production of a lignin-enriched stream for potential valorization. Key criteria for alkaline pretreatment processes, which are important for commercial feasibility, include the minimization of carbohydrate loss during pretreatment and the ability to capture carbon lost to the liquor stream, much of which will be feedstock dependent. Here, we present a comprehensive study of alkaline pretreatment of switchgrass over NaOH loadings from 35 to 140 mg NaOH/g dry switchgrass and with a constant charge of 0.2% anthraquinone for pretreatment temperatures between 100 and 160 °C for 30 min. Full compositional analysis of the pretreated solids are reported as a function of pretreatment severity, along with the yields of each biomass component present in the process streams generated during pretreatment (pretreated solid, liquor, and wash fraction). The pretreated solids are further characterized through crystallinity measurements and electron microscopy. Additionally, enzymatic digestions of the residual solids are performed over a range of enzyme loadings for varying pretreatment severities. These results are compared to our recent work with alkaline pretreatment of corn stover using the ratio of lignin fractionation to carbohydrate retention (in the solids after pretreatment), which highlights the greater recalcitrance of switchgrass relative to corn stover. Specifically, compared to corn stover, switchgrass requires approximately twice the NaOH loading to achieve identical delignification and high enzymatic digestibility. From this work, the optimal pretreatment conditions for switchgrass are suggested to be 154 mg NaOH/g dry switchgrass at 130 °C for 30 min at temperature. The results from these bench-scale experiments will serve as a guide to scale up processes for the optimization of lignin removal while minimizing carbohydrate loss during alkaline pretreatment.
A Concept for the Fabrication of Penetrating Carbon/Silica Hybrid Materials (2000)

Nanostructured carbon/silica hybrid materials and poly(furfuryl alcohol)/silica xerogel are prepared and characterized here. In the key synthetic step, cation-induced polycondensation of furfuryl alcohol occurs simultaneously with a sol–gel process involving tetraethoxysilane and water to yield the xerogel, which is subsequently thermally transformed to the carbon/silica material (see Figure).
[Demonstration of neuronal activities in primary cultures from fetal mouse hypothalamus maintained in a serum-free medium]. (1980)

Fetal neuronal cells dissociated from mouse hypothalamus are able to grow in a serum-free medium for two to four weeks. Several neuronal activities have been measured during the in vitro cell development. Whereas glutamic acid decarboxylase (EC 4.1.1.15) activity disappears, those of thyroliberin (TRH) and tyrosine hydroxylase (EC. 1.14.16.2) remain stable, and acetylcholine transferase one (EC 2.3.1.6) rises earlier than in a serum supplemented medium. These results show that primary cultures grown in serum-free medium offer a promising model for studying neuronal activity differentiation.
Supplementary Figure 5 from Activation of Hematopoietic Stem/Progenitor Cells Promotes Immunosuppression Within the Pre–metastatic Niche (2023)

&lt;p&gt;Myeloid subsets in pre/early metastatic lung&lt;/p&gt;
Large‐Scale Synthesis of Ultrathin Bi2S3 Necklace Nanowires (2008)

Schlanker mit Erfolg! Im Kolloidzustand stabile ultradünne Bi2S3-Nanodrähte (siehe Bild) mit ausgeprägten exzitonischen Eigenschaften, wie sie in Bismutchalkogeniden noch nie beobachtet wurden, und extrem hohen Extinktionskoeffizienten wurden in Gramm-Mengen synthetisiert. Nanostrukturen wie diese haben ein großes Potenzial für thermoelektrische Anwendungen. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2001/2008/z705034_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Management and Prevention of Intraoperative Acetabular Fracture in Primary Total Hip Arthroplasty. (2018)

Intraoperative acetabular fracture (IAF) is a rare complication of primary total hip arthroplasty (THA). Known risk factors include poor bone stock, underreaming of the acetabular bed, and use of elliptic components. There is a paucity of literature on risk factors, treatment strategies, and outcomes of this potentially devastating complication. We studied the incidence of IAF in primary THA at our high-volume institution. We reviewed 21,519 primary THA cases and identified 16 patients (16 hips) with IAFs. Mean follow-up was 4 years (range, 0-10 years). Implant data were recorded, and acetabular components were identified as elliptic modular or hemispheric modular. The institution's IAF rate was 0.0007%. All IAFs were associated with uncemented acetabular components. Sixty-nine percent of the fractures were not appreciated during surgery. All posterior column fractures required operative intervention in the immediate or early (<3 months) postoperative period. Compared with anterior column fractures, posterior column fractures were associated with acetabular component instability and need for additional surgery. In this article, we also present strategies for managing and preventing IAF in primary THA. This rare fracture requires prompt recognition and often necessitates aggressive management. More study is needed to determine how to better manage IAFs.
ChemInform Abstract: Synthesis of 8(R),9(R)‐9‐Deoxo‐4′′‐deoxy‐6,9‐epoxyerythromycin: Potent Motilides. (1999)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Role of granulocytes and monocytes in the polyvinyl chloride‐induced synthesis of interleukin 8, monocyte chemoattractant protein 1, and leukotriene B4 (2005)

In an in vitro whole blood model of artificial surface-induced inflammation, we have studied the contribution of leukocyte populations in the synthesis of inflammatory mediators. This was done by depleting the blood of specific cell types using magnetic beads coated with monoclonal antibodies against leukocyte surface antigens. Synthesis of interleukin 8 (IL-8) was highly dependent on CD15+ cells and was reduced by 80% when these cells were removed from the blood. Correspondingly, IL-8 production showed a high correlation with the concentration of granulocytes (r = 0.77, p < 0.0001). Synthesis of monocyte chemoattractant protein 1 (MCP-1) was dependent on CD14+ cells and was reduced by 35% when these cells were removed from the blood. Correspondingly, MCP-1 production correlated with the concentration of monocytes (r = 0.39, p < 0.0001). Synthesis of leukotriene B4 (LTB4) was highly dependent on CD15+ cells and was reduced by 75% when these cells were removed from the blood. Correspondingly, LTB4 production correlated strongly with the granulocyte concentration (r = 0.54, p < 0.0001). As expected, complement activation was not affected by cell depletion and did not correlate with the concentration of any of the cell types. Thus, artificial surface-induced IL-8 and LTB4 synthesis was almost exclusively granulocyte dependent. However, MCP-1 synthesis was mainly a product of monocytes, although granulocytes and other subpopulations may partly contribute. (c) 2005 Wiley Periodicals, Inc. J Biomed Mater Res, 2005.
A 29K envelope glycoprotein of equine arteritis virus expresses neutralization determinants recognized by murine monoclonal antibodies (1993)

A panel of six neutralizing murine monoclonal antibodies (MAbs) to equine arteritis virus (EAV) was produced. The MAbs were characterized by Western immunoblotting assay and competitive ELISA. The six MAbs identify a single neutralization site on a 29K envelope glycoprotein. Deglycosylation of viral proteins prior to immunoblotting showed that the 29K protein is the glycosylated form of a 20K protein. Equine anti-EAV serum also strongly bound the 29K glycoprotein, as well as an unglycosylated protein of 17K. The equine antisera to EAV blocked the binding of a selected MAb to EAV, whereas normal equine serum did not. Two neutralization-resistant escape mutant (EM) variants of the EAV prototype were produced using MAb 6D10. The phenotypic properties of the EM viruses were characterized by neutralization and immunoblotting assays with two MAbs (6D10 and 5G11). The two MAbs failed to neutralize either EM virus, and they did not react in an immunoblot assay with any proteins of the EM viruses. In contrast, binding of the equine antiserum to viral proteins was equivalent with prototype and EM virus strains. These data clearly indicate that a 29K envelope glycoprotein expresses at least one neutralization determinant of EAV.
Vasoactive Intestinal Peptide-Receptor Imaging for the Localization of Intestinal Adenocarcinomas and Endocrine Tumors (1995)

Virgolini, I; Raderer, M; Kurtaran, A; Angelberger, P; Banyai, S; Yang, Q; Li, S; Banyai, M; Pidlich, J; Niederle, B; Scheithauer, W; Valent, P
Advanced Modular Sub-Atmospheric Hybrid Heat Engine (Phase 1 Final Report) (2020)

The Phase 1 Final Report describes the results of the work completed during the “Advanced Modular Sub-Atmospheric Hybrid Heat Engine” project. The objectives of Phase 1 work were to develop a conceptual design of the turbine-based modular hybrid heat engine (MHHE), including thermodynamic cycle analysis, define the nominal engine component boundary conditions, identify technology gaps, and develop a detailed test plan to address these gaps through bench scale testing in a potential subsequent Phase 2 project. To achieve the project objective, the following activities were performed in Phase 1 work: (1) Market analysis and primary fuel selection, (2) Conceptual design and integrated layout development, (3) Design support and key components characterization, (4) Planning to move technology to pre-commercial demonstration.
Patellofemoral joint contact area increases with knee flexion and weight‐bearing (2004)

Patellofemoral pain is a common and debilitating disorder. Elevated cartilage stress of the patellofemoral joint is hypothesized to play a role in the onset of pain. Estimating cartilage stress requires accurate measurements of contact area. The purpose of this study was to estimate patellofemoral joint contact areas in a group of healthy, pain-free subjects during upright, weight-bearing conditions. Sixteen subjects (8 female, 8 male) were scanned in a GE Signa SP open configuration MRI scanner, which allowed subjects to stand or squat while reclining 25 degrees from vertical with the knee positioned at 0 degrees , 30 degrees , or 60 degrees of flexion. A custom-built backrest enabled subjects to be scanned without motion artifact in both weight-bearing (0.45 body weight per leg) and reduced loading conditions ('unloaded' at 0.15 body weight) at each knee flexion posture. Male subjects displayed mean unloaded patellofemoral joint contact areas of 210, 414, and 520 mm(2) at 0 degrees , 30 degrees and 60 degrees of knee flexion, respectively. Female subjects' unloaded contact areas were similar at full extension (0 degrees ), but significantly smaller at 30 degrees and 60 degrees (p<0.01), with mean values of 269 and 396 mm(2), respectively. When normalized by patellar dimensions (heightxwidth), contact areas were not different between genders. Under weight-bearing conditions, contact areas increased by an average of 24% (p<0.05). This study highlights the differences in patellofemoral joint contact area between gender, knee flexion postures, and physiologic loading conditions.
O1‐10‐04: Escitalopram Decreases Longitudinal CSF ABETA Concentration in Cognitively Normal Subjects age 60‐85 (2016)

In this study we examined the hypothesis that, as in previous transgenic mouse, retrospective human studies (Cirrito et al., 2011) and acute CSF studies in humans (Sheline et al., 2014), chronic dosing of escitalopram would lower CSF levels of amyloid beta (Aβ) levels in humans. Participants in secondary prevention trials for Alzheimer’s disease (AD) will be exposed to a compound for multiple years; thus, particularly in a clinically asymptomatic population, the compound would need to have a proven safety record, as is true for SSRIs. A randomized double-blind placebo controlled study was performed to determine the effect of 20 mg/day of the SSRI antidepressant, escitalopram, on CSF Aβ42 protein levels. Following a baseline lumbar puncture (LP), healthy cognitively normal 60-85 year old male and female volunteers received either placebo or 20 mg/day of escitalopram for 2 weeks. A validated candidate reference mrm mass spectrometry method (Korecka, et al, 2014) was used to measure CSF levels of Aβ42. Placebo (n = 20) and escitalopram (n = 18) treated subjects did not differ on any demographic variables. Escitalopram-treated subjects had significantly greater lowering of mean total Aβ concentrations (1143.38 +/- 601.52 pg/mL baseline to 1004.17 +/- 514.27)), a 10.9% decrease post-escitalopram, compared with placebo-treated (1327.69 +/- 547.62 pg/mL baseline to 1334.98 +/- 493.2 post-placebo), a 2.58% increase (p = 0.011). We corroborate our prior findings in a prospective human study now showing that chronic escitalopram lowers CSF Aβ42 concentrations compared with placebo. Ongoing studies will determine effects following a longer (8 weeks) duration of exposure. The ability to safely decrease Aβ42 concentrations is potentially important as a preventive strategy for AD.
Production of Fatty Acid-Derived Valuable Chemicals in Synthetic Microbes (2014)

Fatty acid derivatives, such as hydroxy fatty acids, fatty alcohols, fatty acid methyl/ethyl esters, and fatty alka(e)nes, have a wide range of industrial applications including plastics, lubricants, and fuels. Currently, these chemicals are obtained mainly through chemical synthesis, which is complex and costly, and their availability from natural biological sources is extremely limited. Metabolic engineering of microorganisms has provided a platform for effective production of these valuable biochemicals. Notably, synthetic biology-based metabolic engineering strategies have been extensively applied to refactor microorganisms for improved biochemical production. Here, we reviewed: (i) the current status of metabolic engineering of microbes that produce fatty acid-derived valuable chemicals, and (ii) the recent progress of synthetic biology approaches that assist metabolic engineering, such as mRNA secondary structure engineering, sensor-regulator system, regulatable expression system, ultrasensitive input/output control system, and computer science-based design of complex gene circuits. Furthermore, key challenges and strategies were discussed. Finally, we concluded that synthetic biology provides useful metabolic engineering strategies for economically viable production of fatty acid-derived valuable chemicals in engineered microbes.
Neurologic Improvement After Thoracic, Thoracolumbar, and Lumbar Spinal Cord (Conus Medullaris) Injuries (2010)

Thoracic (T4-T9) SCIs have the least potential for neurologic improvement. Thoracolumbar (T10-T12) and lumbar (conus) spinal cord have a greater neurologic improvement rate, which might be related to a greater proportion of lower motor neurons. Thus, defining the exact region of injury and potential for neurologic improvement should be considered in future clinical trial design. Combining all anatomic regions of the spine in SCI trials may be misleading if different regions have neurologic improvement at different rates. Over a ten-year period, 95 complete thoracic/thoracolumbar SCI patients had only a 4.1% rate of neurologic improvement, compared with 96.0% for incomplete lumbar (conus) patients and 66.7% to 72.2% for all others.
Validation of International Working Group response criteria in higher‐risk myelodysplastic syndromes: A report on behalf of the MDS Clinical Research Consortium (2020)

The utility of the International Working Group (IWG) 2006 response criteria for myelodysplastic syndromes (MDS) as a surrogate endpoint for outcomes is unclear. We assessed the validity of the IWG 2006 response criteria in a large cohort of higher-risk MDS patients (pts) treated at centers from the MDS Clinical Research Consortium. The best overall response rate (ORR) by IWG 2006 criteria to first-line therapy among 597 evaluable pts was 38% and include complete response (CR) 16%, marrow CR (mCR) 2%, partial response (PR) 10%, hematological improvement (HI) 10%, stable disease (SD) 33%, and progressive disease (PD) 24%. CR was associated with a better overall survival (OS) compared to all other response groups (P < 0.001). Among 470 pts treated with hypomethylating agent (HMA) as first-line therapy, the overall Response Rate, defined as HI or better was 39%. The median OS from time of best response was 21 mo, 8 mo, 14 mo, 12 mo, 13 mo, and 8 mo for CR, mCR, PR, HI, SD, and PD, respectively (P < 0.001). We validated those results in a separate cohort of 539 higher-risk MDS pts treated at Moffitt Cancer Center who received first-line HMA therapy, particularly addressing the value of mCR and mCR+HI. mCR alone without HI, SD, and PD outcomes were inferior to CR, PR, mCR+HI, and HI. In conclusion, CR by IWG 2006 response criteria can be used as a surrogate endpoint for OS in higher-risk MDS pts. Any response associated with restoration of effective hematopoiesis is associated with better outcome.
Comprehensive Antiretroviral Restriction Factor Profiling Reveals the Evolutionary Imprint of the ex Vivo and in Vivo IFN-β Response in HTLV-1-Associated Neuroinflammation (2018)

HTLV-1-Associated Myelopathy (HAM/TSP) is a progressive neuroinflammatory disorder for which no disease-modifying treatment exists. Modest clinical benefit from type I interferons (IFN-α/β) in HAM/TSP contrasts with its recently identified IFN-inducible gene signature. In addition, IFN-α treatment <i>in vivo</i> decreases proviral load and immune activation in HAM/TSP, whereas IFN-β therapy decreases tax mRNA and lymphoproliferation. We hypothesize this "IFN paradox" in HAM/TSP might be explained by both cell type- and gene-specific effects of type I IFN in HTLV-1-associated pathogenesis. Therefore, we analyzed <i>ex vivo</i> transcriptomes of CD4<sup>+</sup> T cells, PBMCs and whole blood in healthy controls, HTLV-1-infected individuals, and HAM/TSP patients. First, we used a targeted approach, simultaneously quantifying HTLV-1 mRNA (HBZ, Tax), proviral load and 42 host genes with known antiretroviral (anti-HIV) activity in purified CD4<sup>+</sup> T cells. This revealed two major clusters ("antiviral/protective" vs. "proviral/deleterious"), as evidenced by significant negative (TRIM5/TRIM22/BST2) vs. positive correlation (ISG15/PAF1/CDKN1A) with HTLV-1 viral markers and clinical status. Surprisingly, we found a significant inversion of antiretroviral activity of host restriction factors, as evidenced by opposite correlation to <i>in vivo</i> HIV-1 vs. HTLV-1 RNA levels. The anti-HTLV-1 effect of antiviral cluster genes was significantly correlated to their adaptive chimp/human evolution score, for both Tax mRNA and PVL. Six genes of the proposed antiviral cluster underwent lentivirus-driven purifying selection during primate evolution (TRIM5/TRIM22/BST2/APOBEC3F-G-H), underscoring the cross-retroviral evolutionary imprint. Secondly, we examined the genome-wide type I IFN response in HAM/TSP patients, following short-term <i>ex vivo</i> culture of PBMCs with either IFN-α or IFN-β. Microarray analysis evidenced 12 antiretroviral genes (including TRIM5α/TRIM22/BST2) were significantly up-regulated by IFN-β, but not IFN-α, in HAM/TSP. This was paralleled by a significant decrease in lymphoproliferation by IFN-β, but not IFN-α treatment. Finally, using published <i>ex vivo</i> whole blood transcriptomic data of independent cohorts, we validated the significant positive correlation between TRIM5, TRIM22, and BST2 in HTLV-1-infected individuals and HAM/TSP patients, which was independent of the HAM/TSP disease signature. In conclusion, our results provide <i>ex vivo</i> mechanistic evidence for the observed immunovirological effect of <i>in vivo</i> IFN-β treatment in HAM/TSP, reconcile an apparent IFN paradox in HTLV-1 research and identify biomarkers/targets for a precision medicine approach.
Erratum: “Effect of thermal processing on silver thin films of varying thickness deposited on zinc oxide and indium tin oxide” [J. Appl. Phys. 105, 063525 (2009)] (2009)

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