gebhart/patrepeval huggingface dataset:
Characterization of biodegraded coals (1988)

Microbial degradation of coals to materials that are soluble in water has been a topic of intensive research for the last few years. The potential for economical recovery of low-grade coals, coupled with possibilities for further upgrading by microbial desulfurization or methanation has spurred intensive research at a number of laboratories. Until very recently, coal biodegradation has been accomplished using low-grade, naturally oxidized coals such as leonardiate, or coals subjected to pretreatment with oxidizing chemicals. The authors have been able to accomplish the biodegradation of bituminous Illinois 6 coal after a pretreatment consisting of air oxidation, using a culture of the fungus Penicillium sp. They report in this paper results of chemical and spectrometric analyses of the starting materials and products from Illinois 6 coal biodegradation, and compare the results with those previously reported from the biodegradation of leonardite.
Effects of herbivory on the growth and reproduction of Picris hieracioides in the Mediterranean region (1999)

Abstract. The impact of herbivorous insects on the growth and reproduction of Picris hieracioides ( Compositae ) was followed in three consecutive years by comparing plants treated with an insecticide and untreated plants in an old‐field population abandoned for 15 yr (P15). In the third year the interactions between herbivory and competition were analysed as well. Pre‐dispersal seed predation of seed heads was investigated in three adjacent old‐fields abandoned for one (P1), 15 (P15) and 40 yr (P40) in the region of Montpellier, France. Fields differed in vegetation cover and floristic composition and also in density and above‐ground biomass of Picris hieracioides plants (from 246 g per plant in P1, 13.3 g in P15, down to 3.3 g in P40, for the first year of study). The cumulative rainfall between January and July, the period of Picris growth, decreased from 1992 to 1994. Moreover, in 1992, three times as much rainfall occurred in May and June – the period of stem elongation – as in 1993 and 1994. As a consequence, environmental stress increased during the study period. Herbivorous invertebrates had a negative effect on the growth and reproduction of individual plants of Picris hieracioides in P15. The effect was not constant with time, being apparent in only two years out of three. These two years (1992 and 1994) had contrasting climatic characteristics, whereas the year with no apparent effect (1993) was climatically intermediate. When herbivory had effects on growth, the insecticide‐treated plants had a significantly higher above‐ground biomass and produced twice as many seed heads as the control plants. There was no interaction between herbivory and competition. The percentage of damaged seed heads was significantly lower in the P1‐field than in the P40‐field. The P15‐field had intermediate levels of predation. Predation on seed heads increased whereas biomass and reproductive output decreased between 1992 and 1994 in the three old‐fields. Therefore, the results on seed predation (but not for above‐ground biomass and reproduction) tend to confirm‘the environmental stress hypothesis’ of Mattson &amp; Haack (1987) that states that plants under stress are more liable to be attacked by grazers.
Telemedicine for antenatal surveillance of high-risk pregnancies with ambulatory and home fetal heart rate monitoring – an update (2003)

Antepartum fetal surveillance is routinely used to assess the risk of fetal death in high-risk pregnancies. Traditionally, testing is performed in the hospital or outpatient clinic by trained medical staff. New equipment is now available that is easy to operate and can be used for self-monitoring of the fetal heart rate (FHR) in the home setting. The tracings are transmitted by modem to a referral center for immediate interpretation by a health provider. The aim of this review was to assess the current data on the application of this new technology with regard to feasibility, access to care, maternal and neonatal outcome, patient and physician satisfaction, and cost-effectiveness.
Energy Allocation by an Annual Plant when the Effects of Seasonality on Growth and Reproduction are Decoupled (1982)

A model of an annual plant is developed in which it is assumed that photosynthate can be allocated to new leaves or seeds, or stored for subsequent allocation to reproduction. Photosynthetic rate and reproductive efficiency are allowed to vary seasonally with the period of maximum photosynthesis preceding the date of maximum reproductive efficiency. Using methods from optimal control theory, the model is solved and the circumstances favoring the storage of materials determined.
Synthesis and X-ray Crystal Structure of New Substituted 3-4′-Bipyrazole Derivatives. Hirshfeld Analysis, DFT and NBO Studies (2021)

A new compounds named 3-4′-bipyrazoles 2 and 3 were synthesized in high chemical yield from a reaction of pyran-2,4-diketone 1 with aryl hydrazines under thermal conditions in MeOH. Compound 2 was unambiguously confirmed by single-crystal X-ray analysis. It crystalizes in a triclinic crystal system and space group P-1. Its crystal structure was found to be in good agreement with the spectral characterizations. With the aid of Hirshfeld calculations, the H…H (54.8–55.3%) and H…C (28.3–29.2%) intermolecular contacts are the most dominant, while the O…H (5.8–6.5%), N…H (3.8–4.6%) and C…C (3.0–4.9%) are less dominant. The compound has a polar nature with a net dipole moment of 6.388 Debye. The BD(2)C31-C32→BD*(2)N4-C34 (27.10 kcal/mol), LP(1)N5→BD*(2)C31-C32 (36.90 kcal/mol), BD(1)C32-C34→BD*(1)C18-C31 (6.78 kcal/mol) and LP(1)N4→BD*(1)N5-C31 (7.25 kcal/mol) are the strongest π→π*, n→π*, σ-σ* and n→σ* intramolecular charge transfer processes, respectively.
Fully Human Antibody Immunoglobulin from Transchromosomic Bovines is Potent Against SARS-CoV-2 Variant Pseudoviruses (2021)

Abstract SAB-185 is a fully human polyclonal anti-SARS-CoV-2 immunoglobulin produced from the plasma of transchromosomic bovines that are hyperimmunized with recombinant SARS-CoV-2 Wuhan-Hu-1 Spike protein. SAB-185 is being evaluated for efficacy in aphase 3 clinical trial. The World Health Organization (WHO) has identified multiple Variants-of-Concern and Variants-of-Interest (VOC/VOI) that have mutations in their Spike protein that appear to increase transmissibility and/or reduce the effectiveness of therapeutics and vaccines, among other parameters of concern. SAB-185 was evaluated using lentiviral-based pseudovirus assays performed in a BSL2 environment that incorporates stable or transient cell lines that express human angiotensin converting enzyme 2 (ACE2) and transmembrane serine protease 2 (TMPRSS2). The results indicate that SAB-185 retained neutralization potency against multiple SARS-CoV-2 pseudovirus variants, including the Delta, Kappa, Lambda and Omicron variants, that have or are supplanting other VOC/VOI in many countries and regions around the world.
Relapse after allogeneic bone marrow transplantation for refractory anemia is increased by shielding lungs and liver during total body irradiation (2001)

Patients with the refractory anemia (RA) subtype of myelodysplastic syndrome who undergo allogeneic bone marrow transplantation (BMT) have a low risk of relapse, but they have a high risk of nonrelapse mortality when prepared with conventional preparative regimens. To try to reduce nonrelapse mortality, we treated 14 RA patients with a modified approach to total body irradiation (TBI) followed by cyclophosphamide (CY) and HLA-identical sibling BMT. Median patient age was 44 years (range, 28 to 65 years). Patients received TBI with shielding of the right lobe of the liver and both lungs followed by electron beam boosts to shielded ribs. Total radiation exposure in nonshielded areas was 12 Gy (n = 10), 10 Gy (n = 3), or 6 Gy (n = 1). After TBI, patients received CY at 120 mg/kg over 2 days, followed by transplantation of unmanipulated bone marrow. All patients initially achieved engraftment with donor cells, although 2 patients had subsequent reemergence of host hematopoiesis without evidence of disease relapse. Five patients died of transplantation-related causes between 22 and 1262 days post-BMT. Four patients relapsed between 157 and 1096 days post-BMT. These 14 patients were compared with 46 historical controls with RA who received conventional CY/TBI or busulfan/CY preparative regimens. Patients in the experimental group had a similar nonrelapse mortality rate compared with the historical control group (29% versus 37%, respectively; P = .8), but a higher relapse rate (34% versus 2%, P = .0004) and a lower disease-free survival (38% versus 61%, P = .16). We conclude that this modified TBI approach is associated with an unacceptably high risk of relapse for patients with RA undergoing BMT.
Author Correction: Clinical phenotypes and outcomes associated with SARS-CoV-2 variant Omicron in critically ill French patients with COVID-19 (2022)

International audience
Analysis of Stop-Gain and Frameshift Variants in Human Innate Immunity Genes (2014)

Loss-of-function variants in innate immunity genes are associated with Mendelian disorders in the form of primary immunodeficiencies. Recent resequencing projects report that stop-gains and frameshifts are collectively prevalent in humans and could be responsible for some of the inter-individual variability in innate immune response. Current computational approaches evaluating loss-of-function in genes carrying these variants rely on gene-level characteristics such as evolutionary conservation and functional redundancy across the genome. However, innate immunity genes represent a particular case because they are more likely to be under positive selection and duplicated. To create a ranking of severity that would be applicable to innate immunity genes we evaluated 17,764 stop-gain and 13,915 frameshift variants from the NHLBI Exome Sequencing Project and 1,000 Genomes Project. Sequence-based features such as loss of functional domains, isoform-specific truncation and nonsense-mediated decay were found to correlate with variant allele frequency and validated with gene expression data. We integrated these features in a Bayesian classification scheme and benchmarked its use in predicting pathogenic variants against Online Mendelian Inheritance in Man (OMIM) disease stop-gains and frameshifts. The classification scheme was applied in the assessment of 335 stop-gains and 236 frameshifts affecting 227 interferon-stimulated genes. The sequence-based score ranks variants in innate immunity genes according to their potential to cause disease, and complements existing gene-based pathogenicity scores. Specifically, the sequence-based score improves measurement of functional gene impairment, discriminates across different variants in a given gene and appears particularly useful for analysis of less conserved genes.
Vitamin B12 deficiency and gastric histopathology in older patients (2005)

Significantly different endoscopic findings and types of gastritis could often be observed in the presence and absence of B12 deficiency. Atrophy, based on endoscopy, and atrophic gastritis, based on histopathology, suggest the presence of B12 deficiency. Gastric histopathology is not influenced by the age, gender, Hct or MCV of the patients.
Identification of Allosteric Peptide Agonists of CXCR4 (2003)

The chemokine receptor CXCR4 is a co-receptor for T-tropic strains of HIV-1. A number of small molecule antagonists of CXCR4 are in development but all are likely to lead to adverse effects due to the physiological function of CXCR4. To prevent these complications, allosteric agonists may be therapeutically useful as adjuvant therapy in combination with small molecule antagonists. A synthetic cDNA library coding for 160,000 different SDF-based peptides was screened for CXCR4 agonist activity in a yeast strain expressing a functional receptor. Peptides that activated CXCR4 in an autocrine manner induced colony formation. Two peptides, designated RSVM and ASLW, were identified as novel agonists that are insensitive to the CXCR4 antagonist AMD3100. In chemotaxis assays using the acute lymphoblastic leukemia cell line CCRF-CEM, RSVM behaves as a partial agonist and ASLW as a superagonist. The superagonist activity of ASLW may be related to its inability to induce receptor internalization. In CCRF-CEM cells, the two peptides are also not inhibited by another CXCR4 antagonist, T140, or the neutralizing monoclonal antibodies 12G5 and 44717.111. These results suggest that alternative agonist-binding sites are present on CXCR4 that could be screened to develop molecules for therapeutic use.
Kicking against the PRCs (2015)

The Polycomb group (PcG) and trithorax group (trxG) genes play crucial roles in development by regulating expression of homeotic and other genes controlling cell fate. Both groups catalyse modifications of chromatin, particularly histone methylation, leading to epigenetic changes that affect gene activity. The trxG antagonizes the function of PcG genes by activating PcG target genes, and consequently trxG mutants suppress PcG mutant phenotypes. We previously identified the ANTAGONIST OF LIKE HETEROCHROMATIN PROTEIN1 (ALP1) gene as a genetic suppressor of mutants in the Arabidopsis PcG gene LIKE HETEROCHROMATIN PROTEIN1 (LHP1). Here, we show that ALP1 interacts genetically with several other PcG and trxG components and that it antagonizes PcG silencing. Transcriptional profiling reveals that when PcG activity is compromised numerous target genes are hyper-activated in seedlings and that in most cases this requires ALP1. Furthermore, when PcG activity is present ALP1 is needed for full activation of several floral homeotic genes that are repressed by the PcG. Strikingly, ALP1 does not encode a known chromatin protein but rather a protein related to PIF/Harbinger class transposases. Phylogenetic analysis indicates that ALP1 is broadly conserved in land plants and likely lost transposase activity and acquired a novel function during angiosperm evolution. Consistent with this, immunoprecipitation and mass spectrometry (IP-MS) show that ALP1 associates, in vivo, with core components of POLYCOMB REPRESSIVE COMPLEX 2 (PRC2), a widely conserved PcG protein complex which functions as a H3K27me3 histone methyltransferase. Furthermore, in reciprocal pulldowns using the histone methyltransferase CURLY LEAF (CLF), we identify not only ALP1 and the core PRC2 components but also plant-specific accessory components including EMBRYONIC FLOWER 1 (EMF1), a transcriptional repressor previously associated with PRC1-like complexes. Taken together our data suggest that ALP1 inhibits PcG silencing by blocking the interaction of the core PRC2 with accessory components that promote its HMTase activity or its role in inhibiting transcription. ALP1 is the first example of a domesticated transposase acquiring a novel function as a PcG component. The antagonistic interaction of a modified transposase with the PcG machinery is novel and may have arisen as a means for the cognate transposon to evade host surveillance or for the host to exploit features of the transposition machinery beneficial for epigenetic regulation of gene activity.
4-1BB/4-1BBL Interaction Promotes Obesity-Induced Adipose Inflammation by Triggering Bidirectional Inflammatory Signaling in Adipocytes/Macrophages (2012)

Obesity-induced adipose inflammation is characterized by recruitment of macrophages to adipose tissue and release of inflammatory cytokines. 4-1BB, a costimulatory receptor, modulates inflammatory processes through interaction with its ligand 4-1BBL on immune cell surfaces. In this study, we examined whether a 4-1BB/4-1BBL interaction between adipocytes and macrophages participates in obesity-induced adipose inflammation. We found that 4-1BB was expressed on adipocytes and was upregulated by obesity-related factors, which also enhanced 4-1BBL expression on macrophages. 4-1BB and/or 4-1BBL agonists, respectively, activated inflammatory signaling molecules (MAPK/IκBα and MAPK/Akt) in adipocytes and macrophages and enhanced the release of inflammatory cytokines (MCP-1, TNF-α, and IL-6). Moreover, disruption of the 4-1BB/4-1BBL interaction decreased the release of inflammatory cytokines from contact cocultured adipocytes/macrophages. These findings indicate that 4-1BB/4-1BBL-mediated bidirectional signaling in adipocytes/macrophages promotes adipose inflammation. 4-1BB and 4-1BBL may be useful targets for protection against obesity-induced adipose inflammation.
The major determinant of the heparin binding of glial cell-line-derived neurotrophic factor is near the N-terminus and is dispensable for receptor binding (2007)

GDNF (glial cell-line-derived neurotrophic factor), and the closely related cytokines artemin and neurturin, bind strongly to heparin. Deletion of a basic amino-acid-rich sequence of 16 residues N-terminal to the first cysteine of the transforming growth factor beta domain of GDNF results in a marked reduction in heparin binding, whereas removal of a neighbouring sequence, and replacement of pairs of other basic residues with alanine had no effect. The heparin-binding sequence is quite distinct from the binding site for the high affinity GDNF polypeptide receptor, GFRalpha1 (GDNF family receptor alpha1), and heparin-bound GDNF is able to bind GFRalpha1 simultaneously. The heparin-binding sequence of GDNF is dispensable both for GFRalpha1 binding, and for activity for in vitro neurite outgrowth assay. Surprisingly, the observed inhibition of GDNF bioactivity with the wild-type protein in this assay was still found with the deletion mutant lacking the heparin-binding sequence. Heparin neither inhibits nor potentiates GDNF-GFRalpha1 interaction, and the extracellular domain of GFRalpha1 does not bind to heparin itself, precluding heparin cross-bridging of cytokine and receptor polypeptides. The role of heparin and heparan sulfate in GDNF signalling remains unclear, but the present study indicates that it does not occur in the first step of the pathway, namely GDNF-GFRalpha1 engagement.
[Follow-up of arteriosclerosis-induced anterior ischemic optic neuropathy]. (1994)

In 22 patients with acute arteriosclerotic anterior ischemic optic neuropathy (AION), examinations were conducted before the start of therapy and between 1 and 3 years later. In the acute stage of the disease the patients were treated with hemodilution for 10 days. The visual acuity improved from 0.2 to 0.4 (median). Compared with the visual acuity before therapy, at the follow-up 1-3 years later visual acuity had improved by 3 lines or more in 11 patients, remained stationary in 9 patients (+/- 1 line), and worsened in 2 patients by 3 lines or more. The visual fields (Goldmann) improved in 8 patients, did not change in 10 patients and worsened in 4 patients. After 1-3 years, 14 patients (64%) showed a sectorial pallor and 8 patients (36%) a diffuse pallor of the optic disc. Videofluorescein angiography revealed hypofluorescent discs in all patients. No difference in arm-retina time (ART) was found between the acute phase (13.0 +/- 3.3 s) and the examination 1-3 years later (13.1 +/- 2.2 s). ART was within normal limits in all patients. The arteriovenous passage time (AVP) dropped significantly, from 2.36 (+/- 0.81) s in the acute phase to 1.91 (+/- 0.56) s 1-3 years later. However, the AVP still did not fall to normal levels (1.45 +/- 0.40 s). Slowed retinal hemodynamics (AVP) with normal ART at the same time suggests a disturbance in microcirculation still present 1-3 years after the acute phase of AION. The rheological parameters (hematocrit, plasma viscosity, erythrocyte aggregation index) did not show any change between examinations.(ABSTRACT TRUNCATED AT 250 WORDS)
Trajectory tracking for unicycle-type and two-steering-wheels mobile robots (1993)

This study uses the photovoice method to explore how persons living with mild-to-moderate dementia perceive neighborhood landmarks and identify characteristics that render these landmarks salient for outdoor navigation. Previous research has highlighted the role of well-designed, stable geographical landmarks in improving the navigability of neighborhoods for persons living with dementia. However, the specific attributes that render landmarks salient have not yet been sufficiently explored, resulting in inadequate evidence-based environmental design guidelines for dementia-friendly communities. To address this gap, a photovoice study was conducted with five community-dwelling persons living with dementia and their care partners, as part of a dementia-friendly neighborhood walking program in the city of Seattle, USA. Photovoice facilitated the exploration of saliency of neighborhood landmarks from an emic perspective by (i) empowering persons living with dementia to identify and take photos of salient landmarks during the group walk and (ii) interpret and reflect on attributes that contributed to saliency using the photos as visual aids in a focus group discussion and survey questionnaire. Participants associated the saliency of landmarks with two groups of attributes: (i) visual distinctiveness, which encompassed physical aspects, such as size, shape, color, texture; and (ii) meaningfulness, which included subjective factors of personal and emotional significance that linked the landmarks to participants' pasts, passions, hobbies, and emotions related to having dementia. Findings suggest that outdoor landmarks should be designed for maximum legibility and noticeability, as well as familiarity, recognizability, and memorability. The evidence from this research also points to the likely positive effect of salient neighborhood landmarks on the community navigation of persons living with dementia.
CPPU (N-(2-chloro-4-pyridinyl)-N’-phenylurea) Enhancement of Cotton Yields (2018)

The gradual depletion of the Ogallala Aquifer under the Southern High Plains of Texas during the past fifty years has resulted in reduced well capacities for cotton irrigation. Water table declines have already led some to shift from irrigated to dryland farming, and many of the remaining wells cannot provide enough water for full irrigation. The present study evaluated the effectiveness of the synthetic cytokinin CPPU (N-(2-chloro-4-pyridinyl)-N’-phenylurea) on the stimulation of lateral root production and enhancement of cotton yields under dryland conditions. Seed treatments of 250 µmol/mol or seedling sprays of 5 µmol/mol at the cotyledon stage, increased lateral root production. Cotton yield increases associated with the increased rooting ranged from 8 to 20% in three years of field studies under dryland conditions. The greatest yield increases were associated with dry shallow soils. Evaluation of water-deficit stress levels in untreated and CPPU-treated cotton showed reduced water-deficit stress levels throughout the growing season in the CPPU-treated cotton. This study showed that application of CPPU to cotton, early in development, has the potential to reduce water stress and increase yields.
Erratum: Emission of particle unstable resonances from compound nuclei (1984)

The two-body phase space factor in Eq. (3.2) should read as follows: