gebhart/patrepeval huggingface dataset:
Skeletal unloading induces selective resistance to the anabolic actions of growth hormone on bone (1995)

Loss of skeletal weight bearing or physical unloading of bone in the growing animal inhibits bone formation and induces a bone mineral deficit. To determine whether the inhibition of bone formation induced by skeletal unloading in the growing animal is a consequence of diminished sensitivity to growth hormone (GH) we studied the effects of skeletal unloading in young hypophysectomized rats treated with GH (0, 50, 500 micrograms/100 g body weight/day). Skeletal unloading reduced serum osteocalcin, impaired uptake of 3H-proline into bone, decreased proximal tibial mass, and diminished periosteal bone formation at the tibiofibular junction. When compared with animals receiving excipient alone, GH administration increased bone mass in all animals. The responses in serum osteocalcin, uptake of 3H-proline and 45Ca into the proximal tibia, and proximal tibial mass in non-weight bearing animals were equal to those in weight bearing animals. The responses in trabecular bone volume in the proximal tibia and bone formation at the tibiofibular junction to GH, however, were reduced significantly by skeletal unloading. Bone unloading prevented completely the increase in metaphyseal trabecular bone normally induced by GH and severely dampened the stimulatory effect (158% vs. 313%, p < 0.002) of GH on periosteal bone formation. These results suggest that while GH can stimulate the overall accumulation of bone mineral in both weight bearing and non-weight bearing animals, skeletal unloading selectively impairs the response of trabecular bone and periosteal bone formation to the anabolic actions of GH.
Permanent fine tuning of silicon microring devices by femtosecond laser surface amorphization and ablation (2013)

We demonstrate the fine tuning capability of femtosecond laser surface modification as a permanent trimming mechanism for silicon photonic components. Silicon microring resonators with a 15 µm radius were irradiated with single 400 nm wavelength laser pulses at varying fluences. Below the laser ablation threshold, surface amorphization of the crystalline silicon waveguides yielded a tuning rate of 20 ± 2 nm/J · cm(-2)with a minimum resonance wavelength shift of 0.10nm. Above that threshold, ablation yielded a minimum resonance shift of -1.7 nm. There was some increase in waveguide loss for both trimming mechanisms. We also demonstrated the application of the method by using it to permanently correct the resonance mismatch of a second-order microring filter.
Programming of neural progenitors of the adult subependymal zone towards a glutamatergic identity by <i>Neurogenin2</i> (2017)

ABSTRACT While the adult subependymal zone (SEZ) harbors pools of distinct neural stem cells that generate different types of GABAergic interneurons, a small progenitor population in the dorsal SEZ expresses Neurog2 and gives rise to glutamatergic neurons. Here we investigated whether SEZ progenitors can be programmed towards glutamatergic neurogenesis through forced expression of Neurog2. Retrovirus-mediated expression of Neurog2 induced the glutamatergic neuron lineage markers Tbr2 and Tbr1 in cultured SEZ progenitors which subsequently differentiated into functional glutamatergic neurons. Likewise, retrovirus-mediated expression of Neurog2 in dividing SEZ progenitors within the adult SEZ induced Tbr2 and Tbr1 expression, hallmarking entry into the glutamatergic lineage also in vivo. Intriguingly, Neurog2 -expressing progenitors failed to enter the rostral migratory stream (RMS) and instead differentiated directly within the SEZ or the adjacent striatum. In sharp contrast, lentivirus-mediated postmitotic expression of Neurog2 failed to reprogram early SEZ neurons, which instead maintained their GABAergic identity and migrated along the RMS towards the olfactory bulb. Thus, our data show that Neurog2 can program SEZ progenitors towards a glutamatergic identity, but fails to reprogram their postmitotic progeny. Summary statement Our study identifies a critical developmental time window during which progenitors of the adult subependymal zone, specified for generating GABAergic neurons, can be reprogrammed towards glutamatergic neurogenesis.
Collision-Induced Dissociative Crosslinking Reagents and Methodology for the Structural Analysis of Proteins and Protein-Protein Interactions using Tandem Mass Spectrometry. (2008)

Chemical crosslinking combined with mass spectrometry is a viable approach to study the low-resolution structure of proteins as well as the topological organization of protein-protein complexes. The identification of the residues involved in the crosslink, however, remains analytically challenging due to the nature of the crosslink itself and its influence on the resulting mass spectrum. To address these challenges, we have developed a novel class of collision-induced dissociative chemical crosslinking reagents which incorporate a gas-phase cleavable aspartyl-prolyl bond into the linker region of the reagent. \nThe specific dissociation of the crosslinked complex allows for a tandem mass spectrometry analysis to be performed on each of the individual peptides involved in the crosslink and therefore simplifies the analysis of the crosslinked products. Following a description of the organic synthesis and purification protocols developed for two collision-induced dissociative crosslinking reagents, a systematic dissociation study of various lysine containing polyalanine peptides was conducted to determine optimized energies for reagent dissociation. Once optimal conditions had been established, methodologies for incorporating the novel crosslinking reagents into automated high-performance liquid chromatography-tandem mass spectrometry analysis were developed on various mass spectrometry platforms and validated with several different model protein systems. To apply our novel crosslinking reagent and methodology to a structurally unknown protein system, a complete crosslinking study of the transition-state regulator AbrB from Bacillus subtilis was conducted. The structural constraints obtained from these crosslinking studies were used to generate a three-dimensional model of full length AbrB which will serve as a platform for additional biochemical studies.
Domain-wall dynamics in garnet films with orthorhombic anisotropy (1983)

The dynamics of domain walls in (110) oriented manganese containing garnet films have been studied. Bubble films and special films in which a single straight domain wall can be stabilized have been prepared. The magnetic anisotropy in these films is orthorhombic and the influence of the in-plane anisotropy field on the maximum domain-wall velocity has been studied. The observed maximum velocities, varying between 40 and 1500 m s−1, are usually considerably lower than the maximum velocities predicted by theory. However, for very high in-plane anisotropy fields the experimental maximum velocities approximate the theoretical ones. From the comparison of different samples it has been concluded that the maximum velocity of the bubbles having no Bloch lines is not very different from the maximum velocity of straight domain walls. Furthermore, it has been shown that the maximum velocity is independent of the film thickness. The influence of external in-plane fields on the maximum velocity also has been studied. In-plane fields in the hard direction of magnetization have no influence on the maximum velocity. In-plane fields small compared with the in-plane anisotropy field increase the maximum velocity considerably if these in-plane fields are applied in the direction perpendicular to the hard axis of magnetization. The influence of stray fields on the maximum velocity is discussed.
[Foot replantation followed by tibial lengthening. Apropos of a case]. (1991)

The authors present a foot replantation case at the ankle level followed six months later by a tibial lengthening using the Ilizarov procedure. Performing the aforementioned lengthening following a replantation enables good nervous and vascular sutures, tension-free and ensures a satisfactory result.
Minimal residual disease analysis in children with t(12;21)-positive acute lymphoblastic leukemia: comparison of Ig/TCR rearrangements and the genomic fusion gene. (2006)

Quantification of minimal residual disease (MRD) based on clonotypic immunoglobulin/ T-cell receptor (Ig/TCR) gene rearrangements is widely used as an independent prognostic parameter in childhood acute lymphoblastic leukemia (ALL). In this study we compared MRD by quantification of Ig/TCR targets and genomic ETV6-RUNX1 specific sequences. In ten of twelve patients with t(12;21)+ ALL we observed concordance with rapid blast reduction in nine, and high-level persistence in one case. The two remaining patients showed low-level persistence of the genomic breakpoint specific sequence. These patients have remained in complete remission for 38 and 41 months, so far, indicating that a small ETV6-RUNX1-positive clone is not detrimental to the short-term prognosis of affected children.
Possible Role of Stresses in Inducing Spinal Stenosis—A Long Term Complication Following Disk Excision (1990)

A three-dimensional finite element model of an intact ligamentous lumbar motion segment (L3-4) was used to predict stresses in the pars interarticularis regions of the modeled vertebral bodies. The changes in stresses following disk excision, as compared to the intact model, also were computed. The predicted results show an increase in stresses in the posterior bony elements following disk excision. In some patients over a long period of time this increase in stresses, in association with other clinical factors, may lead to bony hypertrophy of the structures that surround the nerve roots. Ultimately, over a long period of time the increase in pressure on the entrapped nerve root may induce recurrent pain and other complications reported in the literature.
Performance of New Homes in a Category 4 Hurricane (2009)

<p>A detailed survey of roof damage in new homes in Punta Gorda Isles, FL caused by Hurricane Charley was undertaken in an earlier study. The homes examined were the larger, concrete/clay tiled roof homes with irregular floor plans and complex roof configurations not explicitly covered by the prevailing wind load codes. The survey showed that the vast majority of the roofs in these houses were undamaged or sustained minor damage. This paper presents results from code-based analyses that attempted to estimate wind forces that were resisted at the critical corner location in these undamaged homes. A parametric study was conducted using ASCE 7-98 in which the building geometry, exposure and wind velocity were varied and the pressure coefficient evaluated. Results showed that connections withstood forces that were significantly higher forces than the design value. Such over-design is especially beneficial for narrow buildings were localized pressures are highest.</p>
Peptide Inhibition of Topoisomerase IB from<i>Plasmodium falciparum</i> (2011)

Control of diseases inflicted by protozoan parasites such as Leishmania, Trypanosoma, and Plasmodium, which pose a serious threat to human health worldwide, depends on a rather small number of antiparasite drugs, of which many are toxic and/or inefficient. Moreover, the increasing occurrence of drug-resistant parasites emphasizes the need for new and effective antiprotozoan drugs. In the current study, we describe a synthetic peptide, WRWYCRCK, with inhibitory effect on the essential enzyme topoisomerase I from the malaria-causing parasite Plasmodium falciparum. The peptide inhibits specifically the transition from noncovalent to covalent DNA binding of P. falciparum topoisomerase I, while it does not affect the ligation step of catalysis. A mechanistic explanation for this inhibition is provided by molecular docking analyses. Taken together the presented results suggest that synthetic peptides may represent a new class of potential antiprotozoan drugs.
Similarity between Copper Resistance Genes from <i>Xanthomonas campestris</i> and <i>Pseudomonas syringae</i> (1993)

Plasmid-borne copper resistance genes from copper-resistant strains of Xanthomonas campestris pv. vesicatoria from California, Florida, and Oklahoma shared structural similarities. A strain of X. campestris pv. campestris also contained plasmid-borne copper resistance genes similar to the resistance genes from X. campestris pv. vesicatoria. Furthermore, a region of the copper resistance genes from X. campestris pv. vesicatoria 07882 hybridized with copA, the first gene of the copper resistance operon (cop) of Pseudomonas syringae pv. tomato. A copper-inducible protein of similar size to CopA was detected by Western blot (immunoblot) analysis from the wild-type strain 07882 and from the cloned copper resistance genes of 07882 introduced into a copper-sensitive strain of X. campestris pv. vesicatoria. A low level of hybridization was observed with chromosomal DNA from other xanthomonads when the copper resistance genes from strain 07882 were used as probes.
Brain Temperature Alters Hydroxyl Radical Production During Cerebral Ischemia/Reperfusion in Rats (1994)

일시적인 뇌의 허혈및 재관류(ischemia/reperfusion)는 특히 해마(hippocampus)의 CA1 pyramidal세포와 dorsolateral striatum의 신경원(neurons)에 선택적인 손상을 일으킨다. 허혈후 뇌손상은 부분적으로 Reactive Oxygen Species(ROS)와 연관이 있으므로 ROS생성의 감소는 저온에 의한 뇌보호의 한 기전으로 작용할 수 있다고 본다. 이 가설을 증명하기 위하여 중심동맥압 35 mmHg의 실혈성 저혈압과 양 경동맥의 일시적 결찰로 가역성 뇌 허혈및 재관류 모델을 만들었으며 15분간의 허혈후 60 간의 재관류를 유지하였다. 뇌온도는 허혈중 30℃, 36℃, 39℃로 유지하였고 재관류후 36-37℃로 유지하였다. 뇌 미세투석(Brain microdialysis)을 이용하여 쥐의 해마에서 HPLC-ECD 방법으로 salicylate의 nonenzymatic hydroxylation(2,3-DHBA)을 측정 하였으며 뇌혈류도 실험중 각군간에 비교하였다. 결과는 허혈중 정상 뇌온도의 쥐에서 salicylate의 대사산물인 2,3-DHBA가 재관류후 60분에 대조치(허혈전)의 251%에 이르렀다. 이러한 2,3-DHBA의 생성의 증가는 허혈중 뇌의 온도가 고온인 경우 재관류후 60분에 대조치의 406%로 강화되었다. 허혈중 뇌의 온도가 저온이었던 쥐에서는 재관류후 60분후에 2,3-DHBA의 생성이 대조치의 160%로 둔화되었다. 뇌혈류는 허혈중 대조치의 약 5%로 감소 되었으나 재관류시 세군 모두에서 대조치의 3-4배로 증가후 정상으로 환원되었으며 통계적으로 유의한 차이가 없었다(P>0.05). 그러므로 2,3-DHBA생성에 대한 허혈시 뇌의 온도는 허혈/재관류중의 뇌혈류에 영향을 받지 않는 것으로 생각된다.
결론: 뇌의 온도변화에 따른 hydroxyl radical 생성의 변화는 쥐의 뇌에서 쉽게 나타나고, 뇌의 허혈중 저온에 의한 hydroxyl radical 생성의 감소는 저온에 의한 뇌보호의 한 기전으로 생각된다.
Photon storage in<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mi>Λ</mml:mi></mml:math>-type optically dense atomic media. II. Free-space model (2007)

In a recent paper [Gorshkov et al., Phys. Rev. Lett. 98, 123601 (2007)], we presented a universal physical picture for describing a wide range of techniques for storage and retrieval of photon wave packets in $\ensuremath{\Lambda}$-type atomic media in free space, including the adiabatic reduction of the photon group velocity, pulse-propagation control via off-resonant Raman techniques, and photon-echo based techniques. This universal picture produced an optimal control strategy for photon storage and retrieval applicable to all approaches and yielded identical maximum efficiencies for all of them. In the present paper, we present the full details of this analysis as well some of its extensions, including the discussion of the effects of non-degeneracy of the two lower levels of the $\ensuremath{\Lambda}$ system. The analysis in the present paper is based on the intuition obtained from the study of photon storage in the cavity model in the preceding paper [Gorshkov et al., previous paper, Phys. Rev. A. 76, 033804 (2007)].
Mechanisms and Specific Directionality of Autotrophic Nitrous Oxide and Nitric Oxide Generation during Transient Anoxia (2010)

The overall goal of this study was to determine the molecular and metabolic responses of chemostat cultures of model nitrifying bacteria to imposition of and recovery from transient anoxic conditions. Based on the study, a specific directionality in nitrous oxide (N(2)O) and nitric oxide (NO) production was demonstrated. N(2)O production was only observed during recovery to aerobic conditions after a period of anoxia and correlated positively with the degree of ammonia accumulation during anoxia. NO, on the other hand, was emitted mainly under anoxia. The production of NO was linked to a major imbalance in the expression of the nitrite reductase gene, which was overexpressed during transient anoxia. In contrast, genes coding for ammonia and hydroxylamine oxidation and nitric oxide reduction were generally under-expressed during transient anoxia. These results are different from the observed parallel expression and activity of nitrite and nitric oxide reductase in heterotrophic bacteria subjected to transient oxygen cycling. Unlike NO, the production of N(2)O could not be solely correlated to gene expression patterns and likely involved responses at the enzyme activity or metabolic levels. Based on experimental data, the propensity of the nitrifying cultures for N(2)O production is related to a shift in their metabolism from a low specific activity (q < q(max)) toward the maximum specific activity (q(max)).
PWE-239 Developing a patient reported outcome measure for symptom assessment in irritable bowel syndrome by experience sampling methodoutcomeof focus groups (2015)

<h3>Introduction</h3> There is a growing need to understand the experience of irritable bowel syndrome (IBS) and factors contributing to its disease burden, from the patient–s perspective. Retrospective end-of-day questionnaires are currently used to assess abdominal pain and other gastrointestinal symptoms in IBS. However, these assessments are influenced by recall bias and psychosocial factors. The Experience Sampling Method (ESM) may overcome these limitations by assessing symptoms randomly and repeatedly in the natural state and environment of the subject. An explorative study from our group demonstrated more accurate measurements of IBS symptom patterns when comparing ESM to retrospective questionnaires. Aim of the current study was to develop a short and balanced patient-reported outcome measure for symptom assessment using ESM based on focus group interviews. <h3>Method</h3> Focus group interviews were conducted to obtain patient input in order to develop an ESM questionnaire, to be administered randomly ten times a day. Participants, meeting Rome III criteria for IBS, were asked to suggest every item they considered relevant. Additionally, subjects were instructed to specifically criticise the ESM questionnaire that was used in our previously performed pilot study. After reaching saturation, the identified items were discussed by local experts in the field of neurogastroenterology in order to develop the final ESM questionnaire. <h3>Results</h3> Four focus group meetings were organised with 4–8 participants attending each session (76.5% female; 54 ± 12.6 years). These revealed seven essential categories: abdominal pain, defecation, provoking and relieving factors, dietary factors, other gastrointestinal symptoms, mood and psychological factors, comorbidities and medication use. In total, the participants disclosed 43 specific questions. Experts reduced these to 25 in order to decrease the time and burden associated with completing the questionnaire. <h3>Conclusion</h3> In this study, a patient-reported outcome measure, suitable for symptom assessment, including possible influencing daily life factors in IBS, was developed. This measure is to be validated in a large, heterogeneous IBS population in order to implement it as a symptom assessment tool to evaluate therapeutic responses. Furthermore, ESM offers a suitable approach to identify daily life triggers for symptoms with potential implications for individualised therapeutic strategies. <h3>Disclosure of interest</h3> None Declared.
Analyzing the structural aspects of Isoprenoid biosynthesis pathway proteins in Ocimum species (2017)

Generally thought that the extremely diverse array of secondary metabolites observed within Ocimum species defends against a comparable diverse array of biotic pests, pathogens and herbivores encountered around its natural range. Along with defense the diverse array of secondary metabolite also leads to the therapeutic and remedial property which justifies Ocimum as natural medicinal and aromatic casket. Many of the defense compounds, aroma compounds and medicinal derivatives are secondary metabolites isolated from trichome glands, mainly consist of terpenoids as well as phenylpropanoids. Various pathways fabricating these compounds are known viz. mevalonate pathway (MVA), phenylpropanoid pathway and MEP pathways. The enzyme cascade responsible for various secondary metabolites, need to be explored in various aspects. Here we had studied the MVA pathway enzymes in O. basilicum and O. gratissimum to figure out variations in enzyme structures due to speciation. Hence, in depth analysis of the transcriptome of O. basilicum and O. gratissimum, varrying in qualitative and quantitative aspects of essential oil were carried out. The transcriptome data from NCBI server was assembled using bioinformatic approaches. nr database at NCBI repository used for annotation, which assigned 60% contigs to known functions. Contigs corresponding to Mevalonate pathway enzymes are isolated using perl pipelines developed in our lab, which were further assembled using CLC workbench to remove redundancy and make larger stretch of sequence. Blastx of these larger sequences assigned them function and they are mapped to validated sequences to make full length. Data from both species led us to overall seven enzymes (total 14) of MVA pathway. These enzymes are studied in detail for various physio-chemical properties, steriochemical properties and motif/domain for protein-protein interaction (PPI) study. Homolog models of all enzymes were predicted, against templates from RCSB database. Threading approach is used for enzymes whose homologs are not available in public domain. Structure analysis (energy minimization, Ramachandran plot, stereospecificity and PDB cleaning, Root Mean Square deviation) helped to infer that amongst seven enzymes key gene from MVA pathway showed variation at three sites with in active domain. This study opens up new avenue for secondary metabolite pathway prediction and operation analysis, this will help to develop biotechnological logical tools for Ocimum crop improvement.
Mechanisms of Radiosensitization in Bromodeoxyuridine-substituted Cells (1993)

The radiosensitization of exponentially-growing V79-171 cells whose DNA has been substituted by bromodeoxyuridine (BrdU) in place of thymidine is decreased if acetone is present during irradiation. Acetone, at a concentration of 1 mol dm-3, removes the majority of the increase in double-strand breaks (dsbs) caused by BrdU substitution, but only removes approximately half of the increase in cell killing. The decrease in cell radiosensitization coincides with the removal of the additional dsbs. The protection afforded by acetone against dsbs is assumed to be due to its ability to scavenge hydrated electrons, thought to be the active species causing the increased DNA damage in the presence of BrdU. The residual component of BrdU radiosensitization which could not be removed by treatment with acetone may be due to either a subset of nonscavengable, lethal dsbs or the influence of BrdU on the fixation of potentially-lethal damage (Iliakis et al. 1992). Cells substituted with BrdU are not sensitized to hydroxyl radicals (from hydrogen peroxide). Also, the enhanced levels of single-strand break (ssb) and dsb production in cells substituted with BrdU arise from analogous events (i.e. increases in the yield of ssbs). These studies support the locally multiply damaged site theory of lesion (dsb) production (Ward 1981) and, in the case of BrdU-substituted cells, the increase in dsbs appears to be due to the production of additional ssbs by hydrated electrons at sites of multiple damage.