gebhart/patrepeval huggingface dataset:
Improving the chances of successful protein structure determination with a random forest classifier (2014)

Obtaining diffraction quality crystals remains one of the major bottlenecks in structural biology. The ability to predict the chances of crystallization from the amino-acid sequence of the protein can, at least partly, address this problem by allowing a crystallographer to select homologs that are more likely to succeed and/or to modify the sequence of the target to avoid features that are detrimental to successful crystallization. In 2007, the now widely used XtalPred algorithm [Slabinski et al. (2007), Protein Sci. 16, 2472-2482] was developed. XtalPred classifies proteins into five `crystallization classes' based on a simple statistical analysis of the physicochemical features of a protein. Here, towards the same goal, advanced machine-learning methods are applied and, in addition, the predictive potential of additional protein features such as predicted surface ruggedness, hydrophobicity, side-chain entropy of surface residues and amino-acid composition of the predicted protein surface are tested. The new XtalPred-RF (random forest) achieves significant improvement of the prediction of crystallization success over the original XtalPred. To illustrate this, XtalPred-RF was tested by revisiting target selection from 271 Pfam families targeted by the Joint Center for Structural Genomics (JCSG) in PSI-2, and it was estimated that the number of targets entered into the protein-production and crystallization pipeline could have been reduced by 30% without lowering the number of families for which the first structures were solved. The prediction improvement depends on the subset of targets used as a testing set and reaches 100% (i.e. twofold) for the top class of predicted targets.
Ueber die Pentasulfide des Rubidiums und Cäsiums (1905)

eiii Gemenge oder pine ~:hernische Vrrbindung darstellt.Auderrrseits \vat-L I I erwarteii, (lass sich unter den Alkalinietallen in besondrrs
Bainite and martensite start temperature calculated with exponential carbon dependence (2011)

Analysis of published data demonstrates that the start temperatures of bainite ( B s ) and martensite ( M s ) formation exhibit an exponential carbon dependence. Empirical models are proposed to describe this specific carbon dependence. The models are relatively simple and sufficiently accurate for conventional steels with 0·1–1·9 wt- carbon and less than 7 wt- in total of other alloying elements. Predictions of the B s and M s temperatures show a better accuracy than those obtained with equations from literature. An improved prediction of the M s temperature is important to accurately determine of the amount of martensite at a certain arrest temperature using the Koistinen and Marburger (KM) equation. Predictions of the volume fraction martensite are also influenced by the rate parameter α m controlling the kinetics of martensite formation. Based on the improved models for the composition dependence of M s and α m , the volume fraction of retained austenite at room temperature has been calculated for Fe–C alloys. The calculated fraction of retained austenite as a function of carbon content is found to be in good agreement with published data, which gives confidence in the proposed models for M s and α m .
Home Economics Women Take the Air (1939)

Gaynold Carroll relates the success story of Iowa State's Homemakers' Half Hour.
Anion Influenced Hydride Formation on Cu(111) during Electrocatalysis (2022)

In aqueous systems several environmentally relevant proton-coupled electron transfer reactions such as the reduction of O 2 , NO 3 , CO or CO 2 are known to proceed on Cu surfaces in combination with proton and/or water reduction. Among these, the electrochemical reduction of CO 2 receives the most attention because of Cu’s unique ability to produce varying degrees of hydrogenated multicarbon products. Despite intense experimental and theoretical studies, understanding of Cu’s facet specific selectivity is still limited especially regarding the role of H in hydrogenation steps. Using operando electrochemical mass spectrometry (ECMS) and shell-isolated nanoparticle enhanced Raman spectroscopy (SHINERS) this work identifies the existence of surface hydride on Cu(111) ( Figure 1a ) under conditions relevant for the aforementioned reduction reactions. The identified surface hydride is significantly impacted to changes in electrolyte composition, such as the cation, anion or dissolved gas species and likely has significant impact over electrocatalytic performance. ECMS plots ( Figure 1b ) of hydride formation and decomposition show that the stronger the binding affinity of the anion to the Cu(111) surface the larger the overpotential required for hydride formation (e.g. Cl - vs ClO 4 - ). Likewise, decomposition occurs at more negative potentials. Peak areas of respective vibrational modes ( Figure 1 c-d ) corroborate the ECMS data, also demonstrating that in the presence of Cl - (vs SO 4 2- ) both hydride formation and decomposition shifts negatively by nearly 100 mV. These dynamics among other more quantitative analysis of hydride coverage and kinetics will be presented within this talk. Figure 1
Three-year outcome of local injection of autologous stromal vascular fraction cells and microfat in refractory perianal fistulas of Crohn’s disease (2022)

Perianal fistulas in Crohn's disease are frequent and disabling, with a major impact on patients' quality of life. Cell-based therapy using mesenchymal stem cells represents new hope for these patients, but long-term efficacy remains challenging. In a pilot study, including patients with refractory complex perianal fistulas, autologous adipose-derived stromal vascular fraction (ADSVF) combined with microfat achieved combined remission in 60% of cases, with a good safety profile at 1 year. The purpose of this study is to assess whether these results were maintained at longer term. The safety and efficacy data of the ten patients were evaluated retrospectively 3 years after injection on the basis of clinical and radiological data. MRI were analysed according to the MAGNIFI-CD score. No adverse event was attributed to the experimental stem-cell treatment. Combined remission was achieved in 7 patients (70%) and associated with a significant improvement in the MAGNIFI-CD MRI score. In conclusion, the safety and efficacy of ADSVF and microfat injection in Crohn's disease fistulas were maintained at 3 years, demonstrating that this innovative strategy is effective in producing a long-lasting healing effect. The ongoing multicentre randomized placebo-controlled trial (NCT04010526) will be helpful to define the place for this approach in the current therapeutic arsenal.
Fullerene Nucleating Agents: A Route Towards Thermally Stable Photovoltaic Blends (2014)

The bulk‐heterojunction nanostructure of non‐crystalline polymer:fullerene blends has the tendency to rapidly coarsen when heated above its glass transition temperature, which represents an important degradation mechanism. We demonstrate that fullerene nucleating agents can be used to thermally arrest the nanostructure of photovoltaic blends that comprise a non‐crystalline thiophene‐quinoxaline copolymer and the widely used fullerene derivative [6,6]‐phenyl‐C 61 ‐butyric acid methyl ester (PCBM). To this end, C 60 fullerene is employed to efficiently nucleate PCBM crystallization. Sub‐micrometer‐sized fullerene crystals are formed when as little as 2 wt% C 60 with respect to PCBM is added to the blend. These reach an average size of only 200 nanometers upon introduction of more than 8 wt% C 60 . Solar cells based on C 60 ‐nucleated blends indicate significantly improved thermal stability of the bulk‐heterojunction nanostructure even after annealing at an elevated temperature of 130 °C, which lies above the glass transition temperature of the blend. Moreover, we find that various other compounds, including C 70 fullerene, single‐walled carbon nanotubes, and sodium benzoate, as well as a number of commercial nucleating agents—commonly used to clarify isotactic polypropylene—permit to control crystallization of the fullerene phase.
Molecular dynamics algorithm for multiple time scales: Systems with long range forces (1991)

A frequently encountered problem in molecular dynamics is how to treat the long times that are required to simulate condensed systems consisting of particles interacting through long range forces. Standard methods require the calculation of the forces at every time step. Because each particle interacts with all particles within the interaction range of the potential the longer the range of the potential the larger the number forces that must be calculated at each time step. In this note we present a variant of the RESPA (reference system propagator algorithm), which we developed for handling systems with multiple time scales like disparate mass mixtures. This version of RESPA greatly reduces the number of forces that must be computed at each time step and thereby leads to a dramatic acceleration of such simulations. The RESPA method uses ideas similar to NAPA, an algorithm we invented to treat high frequency oscillators interacting with low frequency bath. The method is based on a choice of a reference system in which the particles interact through short range forces. The reference system is numerically integrated for n time steps δt and the error incurred by using short range forces is corrected by solving a rigorous set of equations once every Δt=nδt. This method reduces the cpu time dramatically. It is shown that this approach and suitable generalizations should be very useful for future simulations of quantum and classical condensed matter systems.
Increased serum protein levels by Yuanshi Shengmai Chenggu Tablet in treatment of avascular osteonecrosis of the femoral head (2017)

The traditional Chinese medicine (TCM) Yuanshi Shengmai Chenggu Tablet is used for treating the common orthopedic disease, hormone‑induced avascular necrosis of the femoral head (ANFH) in China. However, its underlying mechanism and the changes induced in the treatment of ANFH remain to be fully elucidated. In the present study, through the use of isobaric Tag for Relative and Absolute Quantitation and multiple reaction monitoring quantifications, corticosteroid‑induced femoral head necrosis and the effects of treatment with Yuanshi Shengmai Chenggu Tablet were examined. The aim was to identify serum proteins, which may be potential serum markers for the early clinical diagnosis of ANFH, and maybe used to develop more rapid and convenient detection strategies. A total of five proteins were identified, comprising Ig mu chain C region, keratin, type I cytoskeletal 9, properdin, apolipoprotein A‑IV, and IQ and AAA domain‑containing protein 1. The expression levels of all five proteins were lower in ANFH and were higher following TCM treatment. These findings were confirmed using ELISA and western blot analysis.
Haptic Data Compression and Communication (2010)

The past decade has witnessed how audio-visual communication has shaped the way humans interact with or through technical systems. In contemporary times, the potential of haptic communication has been recognized as being compelling to further augment human-to-human and human-to-machine interaction. In the context of immersive communication, video and audio compression are considered key enabling technologies for high-quality interaction. In contrast, the compression of haptic data is a field of research that is still relatively young and not fully explored. This disregards the fact that we as humans rely heavily on the haptic modality to interact with our environment. True immersion into a distant environment and efficient collaboration between multiple participants both require the ability to physically interact with objects in the remote environment. With recent advances in virtual reality, man-machine interaction, telerobotics, telepresence, and teleaction, haptic communication is proving instrumental in enabling many novel applications. The goal of this overview article is to summarize the state of the art and the challenges of haptic data compression and communication for telepresence and teleaction.
Supplementary Data from Discovery, Validation, and Application of Novel Methylated DNA Markers for Detection of Esophageal Cancer in Plasma (2023)

&lt;p&gt;Supplemental Figure 1. Plots of individual methylated DNA marker level distributions with respect to control versus case, further divided by stage.&lt;/p&gt;
Diffusion-mediated in situ alginate encapsulation of cell spheroids using microscale concave well and nanoporous membrane (2011)

Here, we present a novel and simple process of spheroid formation and in situ encapsulation of the formed spheroid without intervention. A hemispherical polydimethylsiloxane (PDMS) micromold was employed for the formation of uniform sized spheroids and two types of nano-porous membrane were used for the control of the crosslinking agent. We characterized the transport properties of the membrane, and the selection of alginate hydrogel as a function of gelation time, alginate concentration, and membrane type. Using the developed process and micromold, HepG2 cell spheroids were successfully formed and encapsulated in alginate without replating. This method allows spheroid encapsulation with minimal damage to the spheroid while maintaining high cell viability. We demonstrate the feasibility of this method in developing a bio-artificial liver (BAL) chip by evaluating viability and function of encapsulated HepG2 spheroids. This method may be applied to the encapsulation of several aggregating cell types, such as β-cells for islet formation and stem cells for embryonic body preservation, or as a model for tumor cell growth and proliferation in a 3D hydrogel environment.
Supplementary Table from FOXR2 Is an Epigenetically Regulated Pan-Cancer Oncogene That Activates ETS Transcriptional Circuits (2023)

Supplementary Table from FOXR2 Is an Epigenetically Regulated Pan-Cancer Oncogene That Activates ETS Transcriptional Circuits
Spatiotemporal Control of Vascular Ca V 1.2 by α1 C S1928 Phosphorylation (2022)

These results suggest that PKA-dependent S1928 phosphorylation promotes the spatial reorganization of vascular α1<sub>C</sub> into "superclusters" upon hyperglycemia and diabetes. This triggers Ca<sub>V</sub>1.2 activity and cooperativity, directly impacting vascular reactivity. The results may lay the foundation for developing therapeutics to correct Ca<sub>V</sub>1.2 and arterial function during diabetic hyperglycemia.
Carcinoma of the Thyroid With Ewing Family Tumor Elements and Favorable Prognosis (2013)

The rare reports of primary, nonneuroendocrine small cell carcinomas of the thyroid have not provided enough evidence to support the recognition of these tumors as an entity or to understand their etiopathogenesis. We report the second case of a primary, nonneuroendocrine small cell carcinoma of the thyroid displaying diffuse expression of cytokeratins, CD99, and p63, in the absence of vimentin expression, in a 24-year-old male who is alive without any signs of disease 13 years after total thyroidectomy and radioactive iodine. The tumor disclosed the EWSR1-FLI1 rearrangement, and we propose to designate it as a carcinoma of the thyroid with Ewing family tumor elements.
Environmental-Based Characterization of SoC-Based Instrumentation Systems for Stratified Testing (2005)

This paper proposes a novel environmental-based method for evaluating the good yield rate (GYR) of systems-on-chip (SoC) during fabrication. Testing and yield evaluation at high confidence are two of the most critical issues for the success of SoC as a viable technology. The proposed method relies on different features of fabrication, which are quantified by the so-called Fabrication environmental parameters (EPs). EPs can be highly correlated to the yield, so they are analyzed using statistical methods to improve its accuracy and ultimately direct the test process to an efficient execution. The novel contributions of the proposed method are: 1) to establish an adequate theoretical foundation for understanding the fabrication process of SoCs together with an assurance of the yield at a high confidence level and 2) to ultimately provide a realistic approach to SoC testing with an accurate yield evaluation. Simulations are provided to demonstrate that the proposed method significantly improves the confidence interval of the estimated yield as compared with existing testing methodologies such as random testing (RT).
Chemical Kinetics in Real Time: Using the Differential Rate Law and Discovering the Reaction Orders (1996)

The reaction between 2,4-dinitrochlorobenzene and piperidine to form 2,4-dinitrophenylpiperidine in ethanol is a very suitable experiment for the undergraduate physical chemistry laboratory. The reaction, being first order with respect to each reactant, exhibits overall second-order kinetics. In this paper we describe the kinetic anlysis, in real time, of the spectrometrically-acquired rate data based on the differential rate law, where no assumptions in initial reactant concentrations are necessary, except for their values. The use of scientific spreadsheets for the numerical differentiation and regression analysis is discussed. A distinctive advantage in analyzing the data this way is that it allows the student to "discover" the order of the reaction with respect to each reactant, and hence the rate law.
C825T Polymorphism of the G Protein β 3 -Subunit and Antihypertensive Response to a Thiazide Diuretic (2001)

The T allele of the C825T polymorphism of the gene encoding the beta(3)-subunit of G proteins has been associated with increased sodium-hydrogen exchange and low renin in patients with essential hypertension. To assess its association with blood pressure response to diuretic therapy, we measured the C825T polymorphism in 197 blacks (134 men, 63 women) and 190 non-Hispanic whites (76 men, 114 women) with essential hypertension (mean+/-SD age 48+/-7 years), who underwent monotherapy with hydrochlorothiazide for 4 weeks. Mean declines in systolic and diastolic blood pressures were 6+/-2 (P:<0.001) and 5+/-1 (P:<0.001) mm Hg greater, respectively, in TT than in CC homozygotes. Responses in heterozygotes were intermediate between the homozygous groups. Other univariate predictors of greater blood pressure responses included black race, female gender, higher pretreatment blood pressure, older age, lower waist-to-hip ratio, and measures of lower renin-angiotensin-aldosterone system activity. After the effects of the other predictors were considered, the TT genotype remained a significant predictor of greater declines in systolic and diastolic blood pressures. Thus, the C825T polymorphism of the G protein beta(3)-subunit may help identify patients with essential hypertension who are more responsive to diuretic therapy.
A microelectrode study of the influence of electrolyte on the reduction of quinones in aprotic solvents (1998)

Au microdisc electrodes are used to extend previous studies of the influences of the electrolyte on the voltammetry of quinones, Q, in DMF to solutions with only a low electrolyte concentration. It is shown that the 1e- products, the semiquinones, interact with the cations of all electrolytes studied (Bu4N+, Na+, Li+ and Mg2+) and these interactions are stronger for o-quinones than p-quinones; association constants for ion pairing are reported. The voltammetry for the second 1e- reduction step is largely determined by the solubility of the product, QM2.
Dual gradient LC method for the determination of pharmaceutical residues in environmental samples using a monolithic silica reversed phase column (2006)

Detailed below is a simple reversed-phase liquid chromatography (RP-LC) method for the simultaneous separation of up to 21 acidic, basic, and neutral pharmaceuticals using Merck Chromolith Performance RP-C18e monolithic columns with direct ultraviolet (UV) absorption detection. By simultaneously applying a solvent elution gradient program with a mobile phase flow gradient, both a decrease in the overall analysis time and a general increase in peak efficiencies were observed. Mobile phase pH and buffer concentration were optimised using the overall resolution product under applied gradient conditions. Under optimised conditions peak area reproducibility (n = 6) ranged between 0.4 and 9.3%, determined at the method LOQ level. For real sample analysis pharmaceutical residues were extracted using an optimised solid phase extraction (SPE) procedure, utilising Strata-X extraction cartridges, which overall provided the highest relative recovery data in comparison with four other commercially available SPE sorbents (17 out of 20 residues investigated had recoveries over 70%). Complete method precision, including all sample pre-treatment and LC analysis for six spiked river water samples at the 1 and 2 µg L−1 level was between 10 and 29%. Using 1 L volumes of 1 µg L−1 spiked estuarine water samples, the majority of detection limits were found to be in the 10–50 ng L−1 range.
Tethered naphthalene diimide-based intercalators for DNA triplex stabilization (2000)

The synthesis and triplex stabilizing properties of oligodeoxyribonucleotides functionalized at the 5'- and/or 3'-termini with a naphthalene diimide-based (NDI) intercalator is described. The NDI intercalator was prepared in a single step from the corresponding dianhydride and was attached to the 5'-terminus of an oligodeoxyribonucleotide following a reverse coupling procedure. The DMT protecting group was removed and the sequence phosphitylated to generate the phosphoramidite derivative on the 5'-terminus of the support-bound oligodeoxyribonucleotide. The NDI intercalator with a free hydroxyl was then added in the presence of tetrazole. Attachment of the NDI to the 3'-terminus relied upon a tethered amino group that could be functionalized first with the naphthalene dianhydride, which was subsequently converted to the diimide. Using both procedures, an oligonucleo-tide conjugate was prepared having the NDI intercalator at both the 5'- and 3'-termini. Thermal denaturation studies were used to determine the remarkable gain in stability for triplexes formed when the NDI-conjugated oligonucleotide was present as the third strand in the complex.
Identification of a linear neutralization site within the third variable region of the feline immunodeficiency virus envelope (1993)

Synthetic peptides have been used to map linear B-cell epitopes of the third variable (V3) region of the feline immunodeficiency virus (FIV) external membrane glycoprotein gp120. The analysis of sera from naturally and experimentally FIV-infected cats by Pepscan and enzyme immunoassay with four partially overlapping peptides evidenced three antibody-binding domains, two of which mapped in the carboxyl-terminal half of V3. In particular, the V3.3 sequence (Gly-392-Phe-413) turned out to be important for in vitro neutralization of the virus in that the peptide inhibited the FIV-neutralizing activity of pooled immune cat sera, and on the other hand, cat sera raised against this peptide effectively neutralized FIV infectivity for Crandell feline kidney cells.