gebhart/patrepeval huggingface dataset:
De Novo Protein Surface Design: Use of Cation-π Interactions to Enhance Binding between an α-Helical Peptide and a Cationic Molecule in 50 % Aqueous Solution (2002)

The relative position of the Asp and Trp residues in a peptide chain is important for recognizing a tetraguanidinium receptor through hydrogen bonding and cation–π interactions. The molecule not only binds with high affinity (Ka=1.1×108 M−1), it also stabilizes the helical conformation of the peptide (see schematic representation) as demonstrated by NMR and CD spectroscopy. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2002/z17676_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.
Are We Speeding Up or Slowing Down? On Temporal Aspects of Code Velocity (2023)

This paper investigates how the duration of various code review periods changes over a projects' lifetime. We study four open-source software (OSS) projects: Blender, FreeBSD, LLVM, and Mozilla. We mine and analyze the characteristics of 283,235 code reviews that cover, on average, seven years' worth of development. Our main conclusion is that neither the passage of time or the project's size impact code velocity. We find that (a) the duration of various code review periods (time-to-first-response, time-to-accept, and time-to-merge) for FreeBSD, LLVM, and Mozilla either becomes shorter or stays the same; no directional trend is present for Blender, (b) an increase in the size of the code bases (annually 3-17%) does not accompany a decrease in code velocity, and (c) for FreeBSD, LLVM, and Mozilla, the 30-day moving median stays in a fixed range for time-to-merge. These findings do not change with variabilities in code churn metrics, such as the number of commits or distinct authors of code changes.
Estradiol Fatty Acid Esters Occur Naturally in Human Blood (1983)

Treatment of nonpolar ether extracts of human female blood with mild alkali produced more immunoassayable estradiol than the unhydrolyzed extract. Analysis of the serum extracts showed that the substance which released immunoreactive estradiol after hydrolysis has chromatographic properties identical to those of fatty acid esters of estradiol esterified at carbon 17. The physiological role of these previously unknown endogenous esters might be inferred from their structural similarity to synthetic drugs used therapeutically for their prolonged estrogenic action.
The weapon potential of human pathogenic fungi (2006)

With the exception of Coccidioides spp., human pathogenic fungi are not found among lists of microbes with potential for biological warfare and bioterrorism against humans. However, many human pathogenic fungi are easily obtainable from the environment, are highly dispersible and can cause significant disease after inhalation with relatively low inocula. When the biological and pathogenic attributes of certain human pathogenic fungi are considered using a formula for calculating the relative weapon potential of a microbe it is as apparent that some organisms such as Coccidioides spp. are comparable to other microbes for which there is significant concern. Our analysis suggests that the current indifference to fungi as potential biological weapons against human populations is probably a perception engendered by their non-communicability, lack of history of use or development as biological weapons, and a relatively low incidence of symptomatic disease following natural infection. Awareness of the weapon potential of human pathogenic fungi is an important consideration for greater preparedness against the threat posed by biowarfare and bioterrorism.
Expression of Hypoxia-Inducible Factor-1α and -2α in Hypoxic and Ischemic Rat Kidneys (2002)

Oxygen tensions in the kidney are heterogeneous, and their changes presumably play an important role in renal physiologic and pathophysiologic processes. A family of hypoxia-inducible transcription factors (HIF) have been identified as mediators of transcriptional responses to hypoxia, which include the regulation of erythropoietin, metabolic adaptation, vascular tone, and neoangiogenesis. In vitro, the oxygen-regulated subunits HIF-1alpha and -2alpha are expressed in inverse relationship to oxygen tensions in every cell line investigated to date. The characteristics and functional significance of the HIF response in vivo are largely unknown. High-amplification immunohistochemical analyses were used to study the expression of HIF-1alpha and -2alpha in kidneys of rats exposed to systemic hypoxia bleeding anemia, functional anemia (0.1% carbon monoxide), renal ischemia, or cobaltous chloride (which is known to mimic hypoxia). These treatments led to marked nuclear accumulation of HIF-1alpha and -2alpha in different renal cell populations. HIF-1alpha was mainly induced in tubular cells, including proximal segments with exposure to anemia/carbon monoxide, in distal segments with cobaltous chloride treatment, and in connecting tubules and collecting ducts with all stimuli. Staining for HIF-1alpha colocalized with inducible expression of the target genes heme oxygenase-1 and glucose transporter-1. HIF-2alpha was not expressed in tubular cells but was expressed in endothelial cells of a small subset of glomeruli and in peritubular endothelial cells and fibroblasts. The kidney demonstrates a marked potential for upregulation of HIF, but accumulation of HIF-1alpha and HIF-2alpha is selective with respect to cell type, kidney zone, and experimental conditions, with the expression patterns partly matching known oxygen profiles. The expression of HIF-2alpha in peritubular fibroblasts suggests a role in erythropoietin regulation.
Mitochondrial deficiency impairs hypoxic induction of HIF-1 transcriptional activity and retards tumor growth (2017)

Mitochondria can be involved in regulating cellular stress response to hypoxia and tumor growth, but little is known about that mechanistic relationship. Here, we show that mitochondrial deficiency severely retards tumor xenograft growth with impairing hypoxic induction of HIF-1 transcriptional activity. Using mtDNA-deficient ρ0 cells, we found that HIF-1 pathway activation was comparable in slow-growing ρ0 xenografts and rapid-growing parental xenografts. Interestingly, we found that ex vivo ρ0 cells derived from ρ0 xenografts exhibited slightly increased HIF-1α expression and modest HIF-1 pathway activation regardless of oxygen concentration. Surprisingly, ρ0 cells, as well as parental cells treated with oxidative phosphorylation inhibitors, were unable to boost HIF-1 transcriptional activity during hypoxia, although HIF-1α protein levels were ordinarily increased in these cells under hypoxic conditions. These findings indicate that mitochondrial deficiency causes loss of hypoxia-induced HIF-1 transcriptional activity and thereby might lead to a constitutive HIF-1 pathway activation as a cellular adaptation mechanism in tumor microenvironment.
Berichtigung: Discovery of a Cryptic Depsipeptide from Streptomyces ghanaensis via MALDI‐MS‐Guided High‐Throughput Elicitor Screening (2020)

Due to oversight, the authors neglected to reference ap aper by Zhang et al. [1] in the original version of this Communication.Zhang et al. describe the discovery of eudistamide B, an isomeric compound to cinnapeptin from am arine streptomycete, which differs only in the absolute configuration at three residues.Specifically, eudistamide Bc ontains D-Tyr at residue 8(rather than L-Tyr in cinnapeptin) and (2S,3R)-3-OH-Leu at residues 6and 10 (rather than (2S,3S)-3-OH-Leu in cinnapeptin).While slightly different Marfey analysis procedures were used, it is unlikely that either of these procedures led to racemization, as single enantiomers were observed for all amino acids in both compounds with the exception of Tyrincinnapeptin, the origin of which can be explained based on the biosynthetic gene cluster (see Figure 4ofthe Communication).The authors apologize for the missing citation.
Synthesis of Potato Starch-Acrylic-Acid Hydrogels by Gamma Radiation and Their Application in Dye Adsorption (2016)

Several kinds of acrylic-acid-grafted-starch (starch/AAc) hydrogels were prepared at room temperature (27°C) by applying 5, 10, 15, 20, and 25 kGy of gamma radiation to 15% AAc aqueous solutions containing 5, 7.5, and 15% of starch. With increment of the radiation dose, gel fraction became higher and attained the maximum (96.5%) at 15 kGy, above which the fraction got lowered. On the other hand, the gel fraction monotonically increased with the starch content. Swelling ratios were lower for the starch/AAc hydrogels prepared with higher gamma-ray doses and so with larger starch contents. Significant promotions of the swelling ratios were demonstrated by hydrolysis with NaOH:<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" id="M1"><mml:mn fontstyle="italic">13632</mml:mn><mml:mo>±</mml:mo><mml:mn fontstyle="italic">10</mml:mn><mml:mi>%</mml:mi></mml:math>for 15 kGy radiation-dosed [5% starch/15% AAc] hydrogel, while the maximum swelling ratio was ~200% for those without the treatment. The authors further investigated the availability of the starch/AAc hydrogel as an adsorbent recovering dye waste from the industrial effluents by adopting methylene blue as a model material; the hydrogels showed high dye-capturing coefficients which increase with the starch ratio. The optimum dye adsorption was found to be 576 mg per g of the hydrogel having 7.5 starch and 15% AAc composition. Two kinetic models, (i) pseudo-first-order and (ii) pseudo-second-order kinetic models, were applied to test the experimental data. The latter provided the best correlation of the experimental data compared to the pseudo-first-order model.
Aortic Aneurysmal Disease: Assessment of Stent-Graft Treatment—CT versus Conventional Angiography (2000)

CT angiography is the preferred method for establishing the presence of perigraft leakage following treatment of aortoiliac aneurysms with stent-grafts.
An attack on the proactive RSA signature scheme in the URSA ad hoc network access control protocol (2004)

Recently, Luo, et al. in a series of papers [17, 14, 13, 18, 15] proposed a set of protocols for providing ubiquitous and robust access control [URSA] in mobile ad hoc networks without relying on a centralized authority. The URSA protocol relies on the new proactive RSA signature scheme, which allows members in an ad hoc group to make access control decisions in a distributed manner. The proposed proactive RSA signature scheme is assumed secure as long as no more than an allowed threshold of participating members is simultaneously corrupted at any point in the lifetime of the scheme.
Cerium-Doped Lutetium Aluminum Garnet Phosphors and Optically Transparent Ceramics Prepared from Powder Precursors by a Urea Homogeneous Precipitation Method (2008)

Nanosized, purified crystalline-phase cerium-doped lutetium aluminum garnet (LuAG:Ce) phosphors were prepared by the urea homogeneous precipitation method. The obtained phosphors showed much higher dispersivity, a fairly uniform size of about 30 nm, and higher luminescence intensity than those synthesized by a sol–gel combustion process. The radioluminescence spectrum of the phosphors consisted of two emission bands owing to the transitions from the lowest 5d excited state to the 4f ground state of Ce3+. The transmittance in the visible light region of the transparent ceramics fabricated at 1800 °C for 10 h under a higher vacuum of 1.5×10-3 Pa using the prepared powders reached 70% and the attenuation coefficient decreased to 0.116 mm-1, which caused much higher luminescence intensity. Compared with those reported previously, the optical properties of the LuAG:Ce transparent ceramics fabricated in the present work improved markedly.
Multiplexed Proteomics Technology for the Fluorescence Detection of Glycoprotein Levels and Protein Expression Levels Using Pro-Q® Emerald and SYPRO® Ruby Dyes (2005)

Protein glycosylation is increasingly being recognized as one of the most prominent posttranslational modifications associated with malignant transformation and tumorogenesis as well as cell differentiation. The multiplexed proteomics platform is a new technology that permits quantitative, multicolor fluorescence detection of proteins in gels and on Western blots. This methodology allows the sequential determination of both protein expression level changes as well as altered glycosylation patterns within a single experiment. The linear responses of the fluorescent dyes allow rigorous quantitation of changes in protein expression using advanced image analysis software over a broad 3-log linear dynamic range. Global analysis of glycosylation changes can be expanded by dichromatic lectin-based profiling methods for rapidly categorizing glycan branching structure as well as deglycosylation studies employing exo- and endoglycosidases (1,2. The basic principles and methodologies for the multiplexed proteomics technology are explained in this chapter.
Exploring the Hyperparameter Landscape of Adversarial Robustness (2019)

Adversarial training shows promise as an approach for training models that are robust towards adversarial perturbation. In this paper, we explore some of the practical challenges of adversarial training. We present a sensitivity analysis that illustrates that the effectiveness of adversarial training hinges on the settings of a few salient hyperparameters. We show that the robustness surface that emerges across these salient parameters can be surprisingly complex and that therefore no effective one-size-fits-all parameter settings exist. We then demonstrate that we can use the same salient hyperparameters as tuning knob to navigate the tension that can arise between robustness and accuracy. Based on these findings, we present a practical approach that leverages hyperparameter optimization techniques for tuning adversarial training to maximize robustness while keeping the loss in accuracy within a defined budget.
Rapid and Sensitive Determination of Methylxanthines in Commercial Brands of Tea Using Ultra-High-Performance Liquid Chromatography-Mass Spectrometry (2019)

Recently, chromatographic techniques have the potential to be greener in order to reduce the environmental impact. In this work, a new simple, sensitive, efficient, and green analytical method based on UHPLC-MS has been developed for a quick determination of methylxanthines including caffeine, theobromine, and theophylline in tea. Under the optimum conditions, a baseline separation has been achieved within 30 seconds, using isocratic elution consisting of 90% water and only 10% acetonitrile at 0.5 mL/min flow rate (3 mL acetonitrile per hour). The mass spectrometer was operated with the SIR mode in ESI<sup>+</sup>. The developed method was found to be linear in the range of 0.03-5 <i>μ</i>g/mL, with correlation coefficients greater than 0.9995 for the three compounds. The respective values of LOD were found to be 0.025, 0.015, and 0.01 <i>μ</i>g/mL for caffeine, theobromine, and theophylline, respectively. The proposed assay was applied to 30 commercial tea samples of different brands. Both caffeine and theobromine were found in all tea samples with maximum concentration in sample no. 15, corresponding to 32.6 and 2.72 mg/g of caffeine and theobromine, respectively. On the contrary, theophylline was not detected at all in most samples. When compared with all previous studies that dealt with the same compounds in different matrices, the developed method was found to be the fastest, allowing high-throughput analyses with more than 100 samples/h. The results prove that the method is suitable for routine analysis of methylxanthines and to distinguish the quality of tea samples of various brands.
Axial Radiography of the Distal Femur to Assess Rotational Alignment in Total Knee Arthroplasty (2005)

A method for taking an axial radiograph of the distal femur was developed to see the epicondyles and posterior condyles of the femur. It was hypothesized that these radiographs would be acceptable for evaluating rotational alignment in total knee arthroplasty with comparable reproducibility and good correlation to the results obtained with computed tomography images. Radiographs were obtained of 50 knees in 32 patients having total knee arthroplasty. The radiographs were taken while the patients were with the knee in 90 degrees flexion. The angle between the clinical epicondylar axis and the posterior condylar axis (twist angle) was measured and compared with the results obtained by conventional computed tomography. The interobserver variation in the axial radiography was less than or comparable to the computed tomography method. The mean discrepancy between the two methods (+/- standard deviation) was 0.5 degrees +/- 0.4 degrees (range, 0-1.9 degrees ), and a strong correlation was observed. This plain radiography is acceptable for evaluation of femoral component rotation with comparable reproducibility and correlation to the results with computed tomography. It has several advantages regarding cost, radiation dose, and lack of scatter when used for postoperative assessment.
The TLR-4 agonist adjuvant, GLA-SE, improves magnitude and quality of immune responses elicited by the ID93 tuberculosis vaccine: first-in-human trial (2018)

Tuberculosis (TB) is the leading cause of infectious death worldwide. Development of improved TB vaccines that boost or replace BCG is a major global health goal. ID93 + GLA-SE is a fusion protein TB vaccine candidate combined with the Toll-like Receptor 4 agonist adjuvant, GLA-SE. We conducted a phase 1, randomized, double-blind, dose-escalation clinical trial to evaluate two dose levels of the ID93 antigen, administered intramuscularly alone or in combination with two dose levels of the GLA-SE adjuvant, in 60 BCG-naive, QuantiFERON-negative, healthy adults in the US (ClinicalTrials.gov identifier: NCT01599897). When administered as 3 injections, 28 days apart, all dose levels of ID93 alone and ID93 + GLA-SE demonstrated an acceptable safety profile. All regimens elicited vaccine-specific humoral and cellular responses. Compared with ID93 alone, vaccination with ID93 + GLA-SE elicited higher titers of ID93-specific antibodies, a preferential increase in IgG1 and IgG3 subclasses, and a multifaceted Fc-mediated effector function response. The addition of GLA-SE also enhanced the magnitude and polyfunctional cytokine profile of CD4<sup>+</sup> T cells. The data demonstrate an acceptable safety profile and indicate that the GLA-SE adjuvant drives a functional humoral and T-helper 1 type cellular response.
The Atlas of Human Cardiac Anatomy: A free‐access educational website (2012)

The University of Minnesota's Visible Heart® Laboratory has developed a novel free‐access educational website highlighting both functional and static human cardiac anatomy: The Atlas of Human Cardiac Anatomy ( http://www.vhlab.umn.edu/atlas/ ). This website contains freely downloadable footage from over 100 human hearts, with associated text describing these anatomies, and with various related educational tutorials. To collect these images and videos, human hearts (deemed non‐viable for transplant) were obtained from LifeSource (MN) or the U of MN's Bequest Program, as gifts for research from the organ donors and their families. To honor these donations, all obtained/developed educational information has and will be gifted back for the training of interested individuals: which may range from students in K‐12, undergraduates, post‐graduates, cardiovascular residents or fellows, physicians, or patients themselves. This library of heart images and videos, includes those obtained with videoscopes, fiberscopes, ultrasound, fluoroscopy, MRI, and/or CT: from perfusion‐fixed specimens and/or from reanimated specimens using Visible Heart® methodologies (Hill et al., 2001). “The Atlas” is a living website that is updated on a monthly basis with new educational information, images, video footage, and/or requested materials. This project was funded by NIH training grant T32AR007612 and Medtronic, Inc.
Updating the resolution for 16S rRNA OTUs clustering reveals the cryptic cyanobacterial genus and species (2020)

In processing metabarcoding data from the 16S rRNA amplicon sequencing, OTUs were commonly binned at 97% similarity, the criteria was once proposed as the limit for species delimitation for prokaryotes. This numeric guide is rather a tunable parameter and has recently been revised and increased up to 99% threshold facilitated with more 16S rRNA sequences available. In the study, we updated 97% identity to 99% in combination with monophyletic species concept rather than OTUs to evaluate cyanobacterial diversity from 11 freshwaters using metabarcoding technique. The cyanobacterial OTUs were first determined by aligning to the SILVA database, and further reassigned through the evolutionary placement algorithm (EPA). Inferred from the EPA, metabarcoding found diverse cyanobacterial community with at least 70 monophyletic species (113 OTUs) from 18 coccoid, 14 simple filamentous, 10 heterocytous genera, and Prochlorothrix by clustering OTUs at 97% similarity. When updating to 99% similarity, 5 cryptic genera were detected with 3 of them should be revised as new genera for they achieved monophyly in the phylogeny. In addition, updating to 99% similarity also detected 48 cryptic monophyletic species from 9 genera. In conclusion, updating 97% identity to 99% in combination with monophyletic species found cryptic genera and species, and provided a much clearer separation of cyanobacterial community between lakes and reservoirs and also between seasons. The combined methods improved the use of metabarcoding technique to elucidate field cyanobacterial community.
Steroids and terpenoids from the bark and the wood of Entandrophragma Cylindricum (1994)

Bull. Chem. Soc. Ethiop. 1994, 8(1) 15-20.
Synthesis, Structural Characterization and Biological Evaluation of Novel [1,2,4]triazolo [1,5‐b][1,2,4]benzothiadiazine‐benzothiazole Conjugates as Potential Anticancer Agents (2007)

Two series of 10-substituted 5,5-dioxo-5,10-dihydro[1,2,4]triazolo[1,5-b][1,2,4]benzothiadiazine 2-methyl/ethyl sulfanyl benzothiazole derivatives (5a-d) and 10-substituted 5,5-dioxo-5,10-dihydro[1,2,4]triazolo[1,5-b][1,2,4] benzothiadiazine 2-phenoxy benzothiazole derivatives (16a-c) were synthesized and their structures confirmed by NMR, MS, IR and X-ray crystallography. These compounds were evaluated for their cytotoxicity against 60 human tumour cell lines. One of the synthesized compounds (5b) exhibited significant inhibitory activity against most of the cell lines and has been further evaluated for the five-dose screening.
Genetic susceptibility in pituitary adenomas: from pathogenesis to clinical implications (2011)

Pituitary adenomas usually present sporadically, with a multifactorial pathogenesis including somatic mutational events in cancer-related genes. Genetic predisposition implies the presence of germline DNA alterations with a range of impacts on pituitary cell biology, translating into a variable penetrance of the disease. Genetic causes must be considered in the presence of specific clinical settings, such as familial occurrence of pituitary adenoma, with or without extrapituitary diseases, and may also be suspected in young patients (<30 years of age) with macroadenomas. We review the clinical implications of genetic predisposition, with special attention on multiple endocrine neoplasia type 1, Carney complex and familial isolated pituitary adenoma. Genetic screening in selected patients with an apparently sporadic disease is also discussed.