gebhart/patrepeval huggingface dataset:
P624 Vedolizumab can induce clinical remission in patients with chronic antibiotic-refractory pouchitis: A retrospective single-centre experience (2018)

Chronic antibiotic-refractory pouchitis affects up to 15% of patients with ulcerative colitis (UC) following colectomy with ileal pouch-anal anastomosis (IPAA). Therapy with anti-TNF agents has demonstrated efficacy in retrospective series, whereas data on vedolizumab (VDZ) therapy are scarce. We here report efficacy data of VDZ in patients with chronic antibiotic-refractory pouchitis. We retrospectively assessed all records from UC patients who underwent IPAA and were exposed to VDZ thereafter in our tertiary referral centre. Patients enrolled in a placebo controlled phase IV program with VDZ were excluded, as well as patients with a baseline modified pouchitis disease activity index (mPDAI) < 5 or with Crohn’s disease-related complications of the pouch. All patients received VDZ 300 mg IV at Weeks 0, 2, and 6, whereafter maintenance therapy q8 was continued. The primary endpoint, clinically relevant remission defined as a mPDAI <5 and a reduction of overall score ≥2 points from baseline, was assessed at Week 14. Twelve patients were identified (median (interquartile range) mPDAI 8.0 (7–8) at baseline). All but two patients (83.3%) underwent colectomy because of refractory UC and two for high-grade dysplasia. All but one J-pouches were two-stage procedures, constructed 6.4 years (2.8–12.3) prior to inclusion. All patients developed chronic antibiotic-refractory pouchitis after a median of 1.5 years (0.9–7.8), for which they were previously treated with several courses of antibiotics (100%), thiopurines (16.7%), infliximab (50.0%), or adalimumab (33.3%). mPDAI decreased from 8 (7–8) at baseline to 3 (1.5–6) at Week 14 (p = 0.016), resulting in a clinical relevant remission rate of 81.8%. Endoscopic PDAI sub-score dropped from 6 (5–6) to 3 (2–4, p = 0.03). Steroid free clinicalremission was observed in 63.6% of patients, and antibiotic free remission rate was 54.5% at Week 14. No differences in C-reactive protein, haemoglobin or albumin could be found between baseline and Week 14. After a median follow-up of 46 weeks (14.0–105.3), 63.6% of patients were still in clinical remission. Four (33.3%) patients stopped therapy because of primary non-response (n = 2), loss-of response (n = 1) or clinical and endoscopic remission (n = 1). Two patients reported new onset of arthralgia and no other adverse events were reported. In this case series, VDZ was efficacious and safe to induce clinical remission in patients with chronic antibiotic-refractory pouchitis. Final confirmation is expected via an ongoing phase IV, placebo-controlled randomised controlled trial (NCT02790138).
Molecular basis for complement recognition by integrin αXβ2 (2012)

Integrin α(X)β(2) functions as complement receptor for iC3b and mediates recognition and phagocytosis of pathogens. We used negative-stain EM to examine the α(X)β(2) interaction with iC3b. EM class averages of α(X)β(2) in complex with iC3b define the binding sites on both the integrin and iC3b. iC3b contains C3c and thioester domain moieties linked by a long flexible linker. The binding site is on the key ring of the C3c moiety, at the interface between the MG3 and MG4 domains. Similar complexes are seen between α(X)β(2) and the C3c fragment. α(X)β(2) binds through the α(X) αI domain, on the face known to bear the metal ion-dependent adhesion site, at the opposite end of the αI domain from its site of insertion in the β-propeller domain.
Structural features of the invariant chain fragment CLIP controlling rapid release from HLA-DR molecules and inhibition of peptide binding. (1995)

The invariant chain (Ii) prevents binding of ligands to major histocompatibility complex (MHC) class II molecules in the endoplasmic reticulum and during intracellular transport. Stepwise removal of the Ii in a trans-Golgi compartment renders MHC class II molecules accessible for peptide loading, with CLIP (class II-associated Ii peptides) as the final fragment to be released. Here we show that CLIP can be subdivided into distinct functional regions. The C-terminal segment (residues 92-105) of the CLIP-(81-105) fragment mediates inhibition of self- and antigenic peptide binding to HLA-DR2 molecules. In contrast, the N-terminal segment CLIP-(81-98) binds to the Staphylococcus aureus enterotoxin B contact site outside the peptide-binding groove on the alpha 1 domain and does not interfere with peptide binding. Its functional significance appears to lie in the contribution to CLIP removal: the dissociation of CLIP-(81-105) is characterized by a fast off-rate, which is accelerated at endosomal pH, whereas in the absence of the N-terminal CLIP-(81-91), the off-rate of C-terminal CLIP-(92-105) is slow and remains unaltered at low pH. Mechanistically, the N-terminal segment of CLIP seems to prevent tight interactions of CLIP side chains with specificity pockets in the peptide-binding groove that normally occurs during maturation of long-lived class II-peptide complexes.
CO on Pt(335): Vibrational overtones and site dependence of the vibrational Stark effect (1993)

Electron energy loss spectroscopy is used to compare atop CO at two sites on Pt(335): on the flat (111) terrace and on the step edge. The cross section for the C–O stretch overtone of the terrace species is not significantly larger than that of the edge species. Previous experiments have shown that the vibrational frequency of terrace CO responds much less to applied electrostatic field than does edge CO, even though their ir cross sections are about the same. The present experiment shows that CO has similar molecular properties at the two sites: a chemical explanation for the different Stark tuning rates is ruled out. The difference could be due to spatial variation of the electric field. Local screening of almost all the static electric field at terrace sites is one possibility, but a simple jellium model is unable to explain the observed effect. Interaction of the molecular quadrupole moment with the spatially varying field near the surface is also important.
Forward link power control for high altitude platform station W-CDMA system (2002)

The performance of two distance based forward link power control schemes (nth-power-of-distance and optimum power control schemes) are evaluated for high altitude platform station (HAPS) W-CDMA systems. Results show that the power control schemes perform favorably and are able to provide capacity gains of at least 1.86 times as compared to the case without power control. The practical system performance when power control is applied in finite step sizes is also determined via simulation.
Binding sites of Drosophila melanogaster sex peptide pheromones. (2000)

Drosophila melanogaster sex peptide (SP) and Ductus ejaculatorius peptide (DUP99B) are male pheromones transferred in the seminal fluid to the female during copulation. Both reduce sexual receptivity and stimulate oviposition in females. The presence of high-affinity SP and DUP99B binding sites in the female were investigated by incubation of cryostat tissue sections with (125)I-iodinated peptides and subsequent autoradiography. We found that in adult females radiolabeled SP and DUP99B bind to peripheral nerves, the subesophageal ganglion, the cervical connective, to discrete parts of the thoracic ganglion, and to the genital tract. Weak and uniform labeling was detected in the neuropil of the brain and the thoracic ganglion. The labeling pattern in the nervous system suggests binding of the peptides to sensory afferents or glial cells. Scatchard analysis of the binding of (125)I-DUP99B to antennal nerves yielded a dissociation constant K(d) of 6.4 nM. Competition experiments with peptide fragments show that the peptides bind with their homologous C-terminal regions. Binding sites in the nervous system of females are established throughout sexual maturation. Prominent binding of the peptides to afferent nerves suggests modification of sensory input.
MZmine: toolbox for processing and visualization of mass spectrometry based molecular profile data (2006)

MZmine is available under GNU Public license from http://mzmine.sourceforge.net/.
Applications of cavity ring-down spectroscopy to high precision isotope ratio measurement of13C/12C in carbon dioxide (2006)

Recent measurements of carbon isotopes in carbon dioxide using near-infrared, diode-laser-based cavity ring-down spectroscopy (CRDS) are presented. The CRDS system achieved good precision, often better than 0.2 per thousand, for 4% CO2 concentrations, and also achieved 0.15-0.25 per thousand precision in a 78 min measurement time with cryotrap-based pre-concentration of ambient CO2 concentrations (360 ppmv). These results were obtained with a CRDS system possessing a data rate of 40 ring-downs per second and a loss measurement of 4.0 x 10(-11) cm(-1) Hz(-1/2). Subsequently, the measurement time has been reduced to under 10 min. This standard of performance would enable a variety of high concentration (3-10%) isotopic measurements, such as medical human breath analysis or animal breath experiments. The extension of this ring-down to the 2 microm region would enable isotopic analysis at ambient concentrations, which, combined with the small size, robust design, and potential for frequent measurements at a remote site, make CRDS technology attractive for remote atmospheric measurement applications.
A New Clustering Method Based onGeneral Connectivity (1994)

In this paper, we present a novel concept of the general connectivity among cells. While conventional concept considers direct connections only, the new concept considers both the direct and indirect connections among cells leading to a model capturing a more precise relationship among cells. Based on the model, a new parallel clustering approach is proposed and analyzed. Another new concept of the stable cluster is introduced to improve the clustering result. In conjunction with the clustering process, an investigatory procedure which back tracks the cluster development process to check if all clusters are stable is also developed. Initial test runs, using the new clustering approach for placement, yield an encouraging 21.6% reduction on the number of feed‐throughs in a complex ASIC design.
Assessment of foot disease in the home environment of diabetic patients using a new photographic foot imaging device (2009)

The objective of this study was to compare live and photographic assessments of clinical signs of diabetic foot disease using a new photographic foot imaging device. High quality colour photographs of the plantar foot surface were collected in 20 diabetic feet using a prototype device and in 19 diabetic feet using a definitive version of the device with optimized illumination settings. All photographs were assessed independently by four observers for presence of ulceration, abundant callus, or absence of signs and compared with live and repeated photographic assessments of the feet by the same observers. Agreement between assessments was moderate to good for all outcomes using the prototype device (56-92%) and improved using the definitive version of the device (74-100%). The data seem to suggest that important signs of diabetic foot disease can be diagnosed from high quality photographs using the photographic foot imaging device. Intended for use as telemedical monitoring device in the patients' home, frequent remote assessments may potentially contribute to the early recognition and treatment of foot disease, which may prevent further complications.
Involvement of PG2212 Zinc Finger Protein in the Regulation of Oxidative Stress Resistance in Porphyromonas gingivalis W83 (2014)

The adaptation of Porphyromonas gingivalis to H2O2-induced stress while inducible is modulated by an unknown OxyR-independent mechanism. Previously, we reported that the PG_2212 gene was highly upregulated in P. gingivalis under conditions of prolonged oxidative stress. Because this gene may have regulatory properties, its function in response to H2O2 was further characterized. PG2212, annotated as a hypothetical protein of unknown function, is a 10.3-kDa protein with a cysteine 2-histidine 2 (Cys2His2) zinc finger domain. The isogenic mutant P. gingivalis FLL366 (ΔPG_2212) showed increased sensitivity to H2O2 and decreased gingipain activity compared to the parent strain. Transcriptome analysis of P. gingivalis FLL366 revealed that approximately 11% of the genome displayed altered expression (130 downregulated genes and 120 upregulated genes) in response to prolonged H2O2-induced stress. The majority of the modulated genes were hypothetical or of unknown function, although some are known to participate in oxidative stress resistance. The promoter region of several of the most highly modulated genes contained conserved motifs. In electrophoretic mobility shift assays, the purified rPG2212 protein did not bind its own promoter region but bound a similar region in several of the genes modulated in the PG_2212-deficient mutant. A metabolome analysis revealed that PG2212 can regulate a number of genes coding for proteins involved in metabolic pathways critical for its survival under the conditions of oxidative stress. Collectively, our data suggest that PG2212 is a transcriptional regulator that plays an important role in oxidative stress resistance and virulence regulation in P. gingivalis.
Total Synthesis of (+)-cis-Sylvaticin:  Double Oxidative Cyclization Reactions Catalyzed by Osmium (2006)

The double oxidative cyclization of dienes is a viable procedure for making complex natural products containing cis-THF units. A double deprotection/double oxidative cyclization strategy using catalytic osmium tetroxide was used to construct the bisheterocyclic core of cis-sylvaticin and ultimately confirm its structure. The natural product was then prepared by a short sequence of reactions that is exceptionally concise: the final route being just 13 linear steps and 19 chemical operations in total.
Adipocyte-Derived Plasma Protein Adiponectin Acts as a Platelet-Derived Growth Factor-BB–Binding Protein and Regulates Growth Factor–Induced Common Postreceptor Signal in Vascular Smooth Muscle Cell (2002)

The adipocyte-derived plasma protein adiponectin strongly suppressed HASMC proliferation and migration through direct binding with PDGF-BB and generally inhibited growth factor-stimulated ERK signal in HASMCs, suggesting that adiponectin acts as a modulator for vascular remodeling.
Identification of a metabolic signature for multidimensional impairment and mortality risk in hospitalized older patients (2013)

A combination of several metabolic and hormonal adaptations has been proposed to control aging. Little is known regarding the effects of multiple deregulations of these metabolic and hormonal systems in modulating frailty and mortality in hospitalized elderly patients. We measured 17 biological serum parameters from different metabolic/hormonal pathways in 594 hospitalized elderly patients followed up to 1 year who were stratified into three groups according to their multidimensional impairment, evaluated by a Comprehensive Geriatric Assessment (CGA)-based Multidimensional Prognostic Index (MPI). The mortality incidence rates were 7% at 1 month and 21% at 1 year. Our data show that frailty and mortality rate were positively associated with chronic inflammation and with a down-regulation of multiple endocrine factors. Of the 17 biomarkers examined, blood levels of IGF-1, triiodothyronine, C-reactive protein, erythrocyte sedimentation rate, white blood cell and lymphocyte counts, iron, albumin, total cholesterol, and LDL-c were significantly associated with both MPI severity grade and mortality. In multivariate Cox proportional hazard model, the following biomarkers most strongly predicted the risk of mortality (adjusted hazard ratio (HR) per 1 quintile increment in predictor distribution): IGF-1 HR = 0.71 (95% CI: 0.63-0.80), CRP HR = 1.48 (95% CI: 1.32-1.65), hemoglobin HR = 0.82 (95% CI: 0.73-0.92), and glucose HR = 1.17 (95% CI: 1.04-1.30). Multidimensional impairment assessed by MPI is associated with a distinctive metabolic 'signature'. The concomitant elevation of markers of inflammation, associated with a simultaneous reduction in multiple metabolic and hormonal factors, predicts mortality in hospitalized elderly patients.
Percutaneous closure of a coronary aneurysm with a vein‐coated stent (1998)

Coronary artery aneurysm is a rare but recognized complication following percutaneous intervention. We report the formation of such an aneurysm after recanalization with Excimer laser wire of a chronic totally occluded left anterior descending coronary artery and stent implantation and its subsequent treatment using an autologous vein graft-coated stent. Cathet. Cardiovasc. Diagn. 43:308–310, 1998. © 1998 Wiley-Liss, Inc.
Speciation and distribution of P associated with Fe and Al oxides in aggregate-sized fraction of an arable soil (2015)

Abstract. To maximize crop productivity fertilizer P is generally applied to arable soils, a significant proportion of which becomes stabilized by mineral components and in part subsequently becomes unavailable to plants. However, little is known about the relative contributions of the different organic and inorganic P bound to Fe/Al oxides in the smaller soil particles. The alkaline (NaOH-Na2EDTA) extraction with solution 31P-nuclear magnetic resonance (31P-NMR) spectroscopy is considered as a reliable method for extracting and quantifying organic P and (some) inorganic P. However, any so-called residual P after the alkaline extraction has remained unidentified. Therefore, in the present study, the amorphous (a) and crystalline (c) Fe/Al oxide minerals and related P in soil aggregate-sized fractions (&gt; 20, 2–20, 0.45–2 and &lt; 0.45 μm) were specifically extracted by oxalate (a-Fe/Al oxides) and dithionite (DCB, both a- and c-Fe/Al oxides). These soil aggregate-sized fractions with and without the oxalate and DCB pre-treatments were then sequentially extracted by alkaline extraction prior to solution 31P-NMR spectroscopy. This was done to quantify the various chemical P forms which were associated with a- and c-Fe/Al oxides both in alkaline extraction and in the residual P of different soil aggregate-sized fractions. The results showed that overall P contents increased with decreasing size of the soil aggregate-sized fractions. However, the relative distribution and speciation of varying P forms were found to be independent of soil aggregate-size. The majority of alkaline extractable P was in the a-Fe/Al oxide fraction (42–47 % of total P), most of which was orthophosphate (36–41 % of total P). Furthermore, still significant amounts of particularly monoester P were bound to the oxides. Intriguingly, however, Fe/Al oxides were not the main bonding sites for pyrophosphate. Residual P contained similar amounts of total P associated with both a- (10–13 % of total P) and c-Fe oxides (10–12 % of total P) in various aggregate-sized fractions, suggesting that it was likely occluded within the a- and c-Fe oxides in soil. This implies that with the dissolution of Fe oxides, these P may be released and thus available for plants and microbial communities.
Combined use of intersubject and intrasubject controls to distinguish treatment versus patient effect in retrospective studies. (1992)

Clinical researchers seek to eliminate specific subject attributes from becoming confounding variables to distinguish a treatment effect from an underlying patient effect. In prospective studies, the random assignment of subjects into experimental groups results in the equal distribution of subject attributes, thereby eliminating them as confounding variables. Retrospective study designs, often used in prosthodontics research, preclude the random assignment of subjects. This article describes the application of a standard research design that combines the use of intersubject and intrasubject controls to compensate for the potential imbalance in subject attributes in retrospective clinical studies. This approach should help prevent clinical investigators from declaring differences between experimental groups when, in fact, no differences exist.
The Role of VIP in Cornea (2012)

The data showed that endogenous VIP is not requisite for GF or GFR expression in the normal cornea but, after infection, its absence or reduction is critical for their regulation.
Minimal universal two-qubit controlled-NOT-based circuits (2004)

We give quantum circuits that simulate an arbitrary two-qubit unitary operator up to a global phase. For several quantum gate libraries we prove that gate counts are optimal in the worst and average cases. Our lower and upper bounds compare favorably to previously published results. Temporary storage is not used because it tends to be expensive in physical implementations. For each gate library, the best gate counts can be achieved by a single universal circuit. To compute the gate parameters in universal circuits, we use only closed-form algebraic expressions, and in particular do not rely on matrix exponentials. Our algorithm has been coded in $\mathrm{C}++$.
Visual Evaluation of Sperm Motility (2021)

Fresh gel-free semen should be extended as soon as possible to preserve the viability of the spermatozoa and to permit observation of individual sperm motility characteristics. In addition, spermatozoa in a “raw” or undiluted semen sample are often highly concentrated and tend to clump or agglutinate, making an accurate estimate of motility in raw semen difficult or impossible. This chapter gives step-by-step instructions with interpretative information, as well as useful equipment lists for visual evaluation of sperm motility. Ideally, estimates of sperm motility should be made as soon as possible after semen collection. Sperm motility estimates should be made quickly and efficiently after semen collection, especially if the microscope stage is not heated.
Field weighting model for tracking-integrated optics (2014)

The emergent field of tracking-integrated optics enables a potentially low cost concentrating photovoltaic (CPV) implementation, where single-axis module tracking is complemented by an additional degree of freedom within the module Gross module tracking can take on multiple configurations, the most common being rotation about a polar or horizontal North-South oriented axis. Polar-axis tracking achieves >95% sunlight collection compared to dual-axis tracking[6], leaving the tracking-integrated optics to compensate for +/-23.5 seasonal variations. The collection efficiency of N-S horizontal axis tracking is latitude-dependent, with ~90% collection relative to dual-axis tracking at 32.2 latitude. Horizontal tracking at higher latitudes shifts an increasing burden to the tracking-integrated optics, which must operate between two incidence angle extremes: summer solstice sunrise/sunset to winter solstice noon. An important aspect of tracking-integrated lens design is choosing a suitable field weighting to appropriately account for annual DNI received at each angle of incidence. We present a field weighting model, generalized for polar or horizontal module tracking at any latitude, which shows excellent agreement with measured insolation data. This model is particularly helpful for the design of tracking-integrated optics for horizontally-tracked modules, where the correct field weighting is asymmetric and significantly biased away from the normal incidence.