gebhart/patrepeval huggingface dataset:
Recommendations for the Presentation of NMR Structures of Proteins and Nucleic Acids (2016)

: The recommendations presented here are designed to support easier communication of NMR data and NMR structures of proteins and nucleic acids through unified nomenclature and reporting standards. Much of this document pertains to the reporting of data in journal articles; however, in the interest of the future development of structural biology, it is desirable that the bulk of the reported information be stored in computer-accessible form and be freely accessible to the scientific community in standardized formats for data exchange. These recommendations stem from an IUPAC-IUBMB-IUPAB inter-union venture with the direct involvement of ICSU and CODATA. The Task Group has reviewed previous formal recommendations and has extended them in the light of more recent developments in the field of biomolecular NMR spectroscopy. Drafts of the recommendations presented here have been examined critically by more than 50 specialists in the field and have gone through two rounds of extensive modification to incorporate suggestions and criticisms.
The production of mature gametocytes of Plasmodium falciparum in continuous cultures of different isolates infective to mosquitoes (1982)

In vitro gametocytogenesis of Plasmodium falciparum was observed in all 22 isolates established in this laboratory. Gametocytes were produced in variable numbers—up to 3% of red cells—for a limited period of time after which this stage was seen only very sporadically. Complete maturation of microgametocytes in vitro was obtained in all 14 of the isolates that were tested for exflagellation. Up to 88.2% of membrane-fed Anopheles stephensi were infected from material produced in culture. It was also possible to infect A. gambiae and A. freeborni. Addition of fresh red cells and serum to culture material promoted infectivity of gametocytes. Gametocyte infectivity declined rapidly with time in the membrane feeders held at 38 °C.
Physical interactions between Gsx2 and Ascl1 balance progenitor expansion versus neurogenesis in the mouse lateral ganglionic eminence (2020)

The Gsx2 homeodomain transcription factor promotes neural progenitor identity in the lateral ganglionic eminence (LGE), despite upregulating the neurogenic factor Ascl1. How this balance in maturation is maintained is unclear. Here, we show that Gsx2 and Ascl1 are co-expressed in subapical progenitors that have unique transcriptional signatures in LGE ventricular zone (VZ) cells. Moreover, whereas Ascl1 misexpression promotes neurogenesis in dorsal telencephalic progenitors, the co-expression of Gsx2 with Ascl1 inhibits neurogenesis. Using luciferase assays, we found that Gsx2 reduces the ability of Ascl1 to activate gene expression in a dose-dependent and DNA binding-independent manner. Furthermore, Gsx2 physically interacts with the basic helix-loop-helix (bHLH) domain of Ascl1, and DNA-binding assays demonstrated that this interaction interferes with the ability of Ascl1 to bind DNA. Finally, we modified a proximity ligation assay for tissue sections and found that Ascl1-Gsx2 interactions are enriched within LGE VZ progenitors, whereas Ascl1-Tcf3 (E-protein) interactions predominate in the subventricular zone. Thus, Gsx2 contributes to the balance between progenitor maintenance and neurogenesis by physically interacting with Ascl1, interfering with its DNA binding and limiting neurogenesis within LGE progenitors.
Catabolism of lysine in Penicillium chrysogenum leads to formation of 2-aminoadipic acid, a precursor of penicillin biosynthesis (1994)

Penicillium chrysogenum L2, a lysine auxotroph blocked in the early steps of the lysine pathway before 2-aminoadipic acid, was able to synthesize penicillin when supplemented with lysine. The amount of penicillin produced increased as the level of lysine in the media was increased. The same results were observed in resting-cell systems. Catabolism of [U-14C]lysine by resting cells and batch cultures of P. chrysogenum L2 resulted in the formation of labeled saccharopine and 2-aminoadipic acid. Formation of [14C]saccharopine was also observed in vitro when cell extracts of P. chrysogenum L2 and Wis 54-1255 were used. Saccharopine dehydrogenase and saccharopine reductase activities were found in cell extracts of P. chrysogenum, which indicates that lysine catabolism may proceed by reversal of the two last steps of the lysine biosynthetic pathway. In addition, a high lysine:2-ketoglutarate-6-aminotransferase activity, which converts lysine into piperideine-6-carboxylic acid, was found in cell extracts of P. chrysogenum. These results suggest that lysine is catabolized to 2-aminoadipic acid in P. chrysogenum by two different pathways. The relative contribution of lysine catabolism in providing 2-aminoadipic acid for penicillin production is discussed.
Applications of resveratrol in the treatment of gastrointestinal cancer (2022)

Natural product compounds have lately attracted interest in the scientific community as a possible treatment for gastrointestinal (GI) cancer, due to their anti-inflammatory and anticancer properties. There are many preclinical, clinical, and epidemiological studies, suggesting that the consumption of polyphenol compounds, which are abundant in vegetables, grains, fruits, and pulses, may help to prevent various illnesses and disorders from developing, including several GI cancers. The development of GI malignancies follows a well-known path, in which normal gastrointestinal cells acquire abnormalities in their genetic composition, causing the cells to continuously proliferate, and metastasize to other sites, especially the brain and liver. Natural compounds with the ability to affect oncogenic pathways might be possible treatments for GI malignancies, and could easily be tested in clinical trials. Resveratrol is a non-flavonoid polyphenol and a natural stilbene, acting as a phytoestrogen with anti-cancer, cardioprotective, anti-oxidant, and anti-inflammatory properties. Resveratrol has been shown to overcome resistance mechanisms in cancer cells, and when combined with conventional anticancer drugs, could sensitize cancer cells to chemotherapy. Several new resveratrol analogs and nanostructured delivery vehicles with improved anti-GI cancer efficacy, absorption, and pharmacokinetic profiles have already been developed. This present review focuses on the in vitro and in vivo effects of resveratrol on GI cancers, as well as the underlying molecular mechanisms of action.
Bee‐gent: bonding and encapsulation enhancement agent framework for development of distributed systems (2000)

With the recent fast expansion of networks, interconnection of heterogeneous systems via networks is drawing increasing attention. In this context, the authors propose the Bee-gent (Bonding and Encapsulation Enhancement aGENT) agent framework, whose objective is to allow flexible interconnection between legacy systems, databases, and other existing systems by providing coordination and communication functions for distributed system components. With the proposed network, interaction protocols describing interactions between system components are divided between global processing related to problem solving, and component-specific local processing. Coordination between system components in the global processing is ensured through consistent control by mobile mediation agents. This facilitates design and maintenance if the system is modified or extended. In the paper the practical implementation of the proposed system is discussed and specific practical examples are presented to demonstrate the effectiveness of the system. © 2000 Scripta Technica, Syst Comp Jpn, 31(13): 42–56, 2000
Differential quantum well spatial light modulators for high speed optical interconnections and computing (1990)

Spatial light modulators (SLMs) are an important component for neural and digital optical computing, photonic switching, and optical interconnections of electronic circuits. For optical neural computing and some photonic switching applications, the time required to write the SLM can be relatively long. However, for digital optical computing, optical interconnections, and other photonic switching applications, SLMs must operate as fast as possible. For these high speed applications, spatial light modulators based on the quantum confined Stark effect (QCSE) [1] are a good choice. The inherent speed of the QCSE is extremely fast (~50-100s of femtoseconds) [2] . In addition, waveguide modulators and normal incidence reflection modulators have been made with a 3 dB bandwidths as high as 20 GHz [3] and 5.5 GHz [4] respectively. To maximize the total throughput (number of channels times the bit rate of each channel) of an array of devices, each device must have a separate electrical access lead. In this paper, we present results on a 2 × 4 array of differential quantum well spatial light modulators, each with an individual access leads. Although the device array is not large, it was made using the same batch fabrication procedures [5] that have yielded symmetric SEED arrays as large as 64 × 32 [6] , thus the fabrication techniques are extendible to making larger spatial light modulator arrays. The frequency response of the devices had a 3dB bandwidth limit greater than 3 GHz as modulators and greater than 4 GHz as detectors.
Removal of N‐Terminal Blocking Groups from Proteins (1996)

Two enzymatic methods commonly used in N-terminal sequence analysis of blocked proteins are presented in this unit; one uses pyroglutamate aminopeptidase for N(alpha)-pyrrolidone carboxyl-proteins in solution or blotted onto a membrane, and the other uses acylaminoacyl-peptide hydrolase for N(alpha)-acyl-proteins blocked with other acyl groups. A Support Protocol describes a colorimetric assay for pyroglutamate aminopeptidase activity. Sequencing with acylaminoacyl-peptide hydrolase must include fragmentation of the protein before unblocking can be carried out, so procedures are provided for chemically blocking newly generated peptides with either succinic anhydride or phenylisothiocyanate/performic acid. The hydrolase is then applied to the total mixture of peptides, only one of which, the acylated N-terminal peptide, should be a substrate for hydrolase. After incubation, the mixture of peptides is subjected to sequence analysis. Protocols are also provided for unblocking N-terminally blocked proteins using acid-catalyzed hydrolysis or methanolysis, hydrazinolysis, and beta-elimination after acid-catalyzed N-O shift. Alternate protocols describe chemical removal of acetyl and longer-chain alkanoyl groups, as well as formyl groups to open the cyclic imide of pyrrolidone carboxylate.
Determinanten der Kündigungsbereitschaft: Ein Vergleich zweier konflikttheoretischer Paradigmen (1992)

Zusammenfassung In diesem Artikel wird versucht, das Phänomen der Kündigungsbereitschaft mit konflikttheoretischen Paradigmen zu erklären. Der Kündigungswille von Organisationsmitgliedem wird aus dieser Perspektive neben einer Reihe anderer Faktoren als Resultat von Konflikten in Zusammenhang mit dem Arbeitskontext interpretiert. Zur Analyse der Kündigungsbereitschaft bietet sich einerseits die relative Deprivationstheorie, welche Konflikthandeln als Ausdruck von Frustration, Deprivation oder Unzufriedenheit betrachtet, an und andererseits die Kosten-Nutzen-Theorie, die Konflikthandeln als rationales Handeln auffaßt. Die aus diesen Theoriesträngen abgeleiteten Hypothesen werden anhand der Daten einer empirischen Analyse geprüft. Es wurde für verschiedene Subgruppen untersucht, welche Zufriedenheitsmerkmale für die Kündigungsbereitschaft relevant sind. Dabei hat sich herausgestellt, daß für alle Subgruppen jeweils unterschiedliche Faktoren die Kündigungsabsicht determinieren. Die Analyse bringt zum Ausdruck, daß nicht ein Modell allein das Problem der Kündigungsbereitschaft zu lösen vermag, vielmehr leisten sowohl die Theorie der relativen Deprivation als auch die Kosten-Nutzen-Theorie einen wichtigen Beitrag.
<title>Noninvasive temperature monitoring using ultrasound tissue characterization method</title> (2001)

Microwave thermotherapy (MT) is an oncological treatment. At present the invasive thermometer probes are clinically used for temperature measuring during an MT. Any invasive handling of tumors is of high-risk. A new method of noninvasive monitoring of temperature distribution in tissue has been developed. An MT treatment of the experimentally induced pedicle-tumors of the rat was prepared. It consists of an intelligent regulation loop controlling a high frequency (HF) generator according to the maximal measured temperature in the tissue and a special HF MT applicator. The loop is also equipped with an invasive thermometer (4 invasive probes). During the MT treatment the series of ultrasound B-mode images were obtained. The texture parameters were evaluated form the obtained ultrasound images. These parameters were correlated with the invasively measured temperature during the MT session. For 60 rat samples a strong correlation between the mean gray level in the ROIs in the ultrasound pictures and the invasively measured temperature in the range 37-44 degree(s)C (98.6-111.2 F) was found. The correlation coefficient of the mean gray level and the invasively measured temperature is 0.96+/- 0.05. A system for representation of changes of spatial temperature distribution of the whole tumor during MT will be presented.
Sequential cold-sensitive mutations in Aspergillus fumigatus. II. Analysis by the parasexual cycle (1981)

From Aspergillus fumigatus I-21 (ATCC 32722), which grows at temperatures from 12 to 50 degrees C, three multistep, independently derived, cold-sensitive mutants unable to grow at 37 degrees C or below (Cs-37) were obtained by sequential exposure to ethylmethane sulfonate (strain AT2) or N-methyl-N'-nitro-N-nitrosoguanidine (AT1 and AT3). These mutants and ON5, a five-step Cs-37 mutant, were marked by mutations affecting spore color and nutritional requirements and crossed in four combinations by classical parasexual means. The heterokaryons demonstrated partial complementation with respect to auxotrophic requirements (suboptimal growth on minimal medium) and cold sensitivity (growth at 37 degrees C but not at 25 degrees C). Most presumed diploids, formed by exposure of the heterokaryons to d-camphor vapors, showed complete complementation but were unstable, as demonstrated by variations in spore sizes and markedly different ratios of segregant classes derived from different clones. Analysis of the segregants of the diploids or aneuploids, induced by Benomyl, indicated that multiple genes were responsible for cold sensitivity in each Cs-37 mutant, since segregants with various levels of cold sensitivity were obtained. The higher than predicted frequency of reversion to temperatures two or more steps back in the sequence of cold sensitivity mutations suggested that these genes or their products interacted. No Cs-37 segregant yielding a consistently lower frequency of revertants than the original mutants was obtained.
Scene Classification via Learning a Multi-Branch Convolutional Network (2019)

Efficient and accurate classification of high-resolution scene remains a challenge of within-class diversity and between-class similarity due to rich image variations in viewpoint, object pose, spatial resolution and background. To address these issues, we propose a multi-branch convolutional neural network (MB-CNN), which focuses on tackling the problem of learning the appropriate representation of a high-resolution scene that is rich enough to discriminate between different semantic classes. First, pyramid scene parsing network (PSPNet) with minor modification is introduced to gather global object information. Then, an attention net is proposed to highlight transformation invariance and key regions for attention feature extraction. Finally, above two branches are fused with original input branch to learn consistently semantic class information and generate powerful predictions. Our approach achieves better performance favorably against state-of-the-arts on two publicly available scene datasets.
Cloning, heterologous expression and characterization of murine interleukin 1 receptor antagonist protein (1991)

A cDNA coding for the human interleukin 1 receptor antagonist protein (IL 1Ra) was used to clone the corresponding murine cDNA. The nucleotide sequence of the open reading frame coding for the processed form of mIL 1Ra predicted a 152-residue protein that was 77% identical to human IL 1Ra. The cellular and tissue distribution of murine IL 1Ra (mIL 1Ra) transcripts showed high levels in macrophages and skin while lower levels were detected in tissues that contain significant numbers of resident macrophages. The portion of the mIL 1Ra cDNA that codes for the mature form of the protein was placed under the control of a Trp promoter and expressed in E. coli at a level of 37% of total cell protein. The expressed protein was secreted into the periplasm and was purified to homogeneity in a single step by cation-exchange chromatography. Recombinant mIL 1Ra competitively inhibited 125I-labeled IL 1 alpha binding to murine type I IL 1R present on EL4 6.1 cells (Ki value of 0.21 nM) and antagonized IL 1-stimulated co-mitogenesis in murine thymocytes (0.7 x 10(6)-1.1 x 10(6) units/mg).
Rearrangement, Majorization and Stochastic Scheduling (1993)

Rearrangement inequalities, such as the classical Hardy-Littlewood-Polya inequality and the more general Day's inequality, and related majorization results are often useful in solving scheduling problems. Among other things, they are essential for pairwise interchange arguments. Motivated by solving stochastic scheduling problems, we develop stochastic versions of Day's Inequality, over both unrestricted and restricted (specifically, one-cycle) permutations. These lead to a general and unified approach, which we apply to solve the stochastic versions of several classical deterministic scheduling problems. In most cases, the approach leads to new or stronger results; in other cases it recovers known results with new insight. The approach is built upon recent developments in stochastic majorization and multivariate characterization of stochastic order relations.
Effect of nitrogen and phosphorus availability on the growth response ofEucalyptus grandisto high CO2 (1992)

ABSTRACT The response of Eucalyptus grandis seedlings to elevated atmospheric CO 2 concentrations was examined by growing seedlings at either 340 or 660 n mol CO 2 mol ‐1 for 6 weeks. Graded increments of phosphorus and nitrogen fertilizers were added to a soil deficient in these nutrients to establish if the growth response to increasing nutrient availability was affected by CO 2 concentration. At 660 μmol CO 2 mol ‐1 , seedling dry weight was up to five times greater than at 340 μmol CO 2 mol ‐1 . The absolute response was largest when both nitrogen and phosphorus availability was high but the relative increase in dry weight was greatest at low phosphorus availability. At 340 μmol CO 2 mol ‐1 and high nitrogen availability, growth was stimulated by addition of phosphorus up to 76 mg kg 1 soil. Further additions of phosphorus had little effect. However, at 660 μmol CO 2 mol ‐1 , growth only began to plateau at a phosphorus addition rate of 920mg kg ‐1 soil. At 340 μmol CO 2 mol ‐1 and high phosphorus availability, increasing nitrogen from 40 to 160mg kg ‐1 soil had little effect on plant growth. At high CO 2 , growth reached a maximum at between 80 and 160mg nitrogen kg ‐1 soil. Total uptake of phosphorus was greater at high CO 2 concentration at all fertilizer addition rates, but nitrogen uptake was either lower or unchanged at high CO 2 concentration except at the highest nitrogen fertilizer rate. The shoot to root ratio was increased by CO 2 enrichment, primarily because the specific leaf weight was greater. The nitrogen and phosphorus concentration in the foliage was lower at elevated CO 2 concentration partly because of the higher specific leaf weight. These results indicate that critical foliar concentrations currently used to define nutritional status and fertilizer management may need to be reassessed as the atmospheric CO 2 concentration rises.
Commentary: Personalized Health Planning and the Patient Protection and Affordable Care Act: An Opportunity for Academic Medicine to Lead Health Care Reform (2010)

The Patient Protection and Affordable Care Act of 2010 (PPACA) mandates the exploration of new approaches to coordinated health care delivery--such as patient-centered medical homes, accountable care organizations, and disease management programs--in which reimbursement is aligned with desired outcomes. PPACA does not, however, delineate a standardized approach to improve the delivery process or a specific means to quantify performance for value-based reimbursement; these details are left to administrative agencies to develop and implement. The authors propose that coordinated care can be implemented more effectively and performance quantified more accurately by using personalized health planning, which employs individualized strategic health planning and care relevant to the patient's specific needs. Personalized health plans, developed by providers in collaboration with their patients, quantify patients' health and health risks over time, identify strategies to mitigate risks and/or treat disease, deliver personalized care, engage patients in their care, and measure outcomes. Personalized health planning is a core clinical process that can standardize coordinated care approaches while providing the data needed for performance-based reimbursement. The authors argue that academic health centers have a significant opportunity to lead true health care reform by adopting personalized health planning to coordinate care delivery while conducting the research and education necessary to enable its broad clinical application.
Monitoring treatment of retinal angiomatous proliferation by phase resolved Doppler OCT (2016)

Purpose : In contrast to most conventional imaging techniques, Doppler OCT is able to provide depth-resolved information about intra- and transretinal blood flow non-invasively. We performed an exploratory prospective, observational cohort study to evaluate Doppler OCT for monitoring the effect of treatment in patients with retinal angiomatous proliferation (type 3 CNV). Methods : Twelve treatment-naïve patients were included, with a median age of 79 years (range 65-90). They were diagnosed with type 3 CNV based on fundus examination, fluorescein angiography and indocyanine-green angiography. Patients were additionally imaged with an experimental 1040 nm swept-source phase resolved Doppler OCT instrument before and after treatment. Patients were treated with either intravitreal bevacizumab or triamcinolone injection(s) with or without photodynamic therapy (PDT). Abnormal blood flow after treatment was defined as unchanged, decreased or absent. Results : Good quality Doppler OCT images before and after treatment could be obtained in 9 patients. After the first treatment series the type 3 CNV lesion was absent in 7 patients, in 1 patient the Doppler OCT depicted decreased flow in the lesion and 1 patient showed unchanged abnormal blood flow. Only in 1 out of 4 patients complete resolution was seen after a single bevacizumab injection. Combined therapy of bevacizumab with PDT showed complete resolution in 5 out of 5 patients (see figure). Conclusions : Doppler OCT is able to detect changes in abnormal blood flow after treatment of type 3 CNV. This type of imaging may become an important non-invasive monitoring tool for optimizing treatment strategies in type 3 CNV patients and possibly in other types of macular degeneration.