gebhart/patrepeval huggingface dataset:
Mechanisms Associated with Success and Failure of the Anadromous Migration of Atlantic Salmon (2018)

Nearly every animal accomplishes life history tasks that enable growth and fecundity, factors that determine the ultimate fitness of an individual's life, by moving. Migration allows individuals to maximize their potential fitness by exploiting temporal differences in productivity of discrete habitats. Migratory species have high cultural and ecological importance as vectors linking and fertilizing separate ecosystems; however, their reliance on multiple habitats and long-distance movements exposes them to stressors. I applied electronic tagging to observe the behaviour of wild Atlantic salmon, a migratory fish threatened by climate change, habitat destruction, disease, and overexploitation.
Red meat and colon cancer: dietary haem-induced colonic cytotoxicity and epithelial hyperproliferation are inhibited by calcium (2001)

High intake of red meat is associated with increased colon cancer risk. We have shown earlier that this may be due to the high haem content of red meat, because dietary haem increased cytolytic activity of faecal water and colonic epithelial proliferation. Dietary calcium inhibits diet-induced epithelial hyperproliferation. Furthermore, it has been shown that supplemental calcium inhibited the recurrence of colorectal adenomas. Therefore, we studied whether dietary calcium phosphate can exert its protective effects by inhibiting the deleterious effects of haem. In vitro, calcium phosphate precipitated haem and inhibited the haem-induced cytotoxicity. Subsequently, rats were fed diets, differing in haem (0 or 1.3 micromol/g) and calcium phosphate content only (20 or 180 micromol/g). Faeces were collected for biochemical analyses. Cytolytic activity of faecal water was determined from the degree of lysis of erythrocytes by faecal water. Colonic epithelial proliferation was measured in vivo using [(3)H]thymidine incorporation. In rats fed low calcium diets, dietary haem increased cytolytic activity of faecal water (98 +/- 1 versus 1 +/- 1%, P < 0.001) and the concentration of cations in faeces (964 +/- 31 versus 254 +/- 20 micromol/g), when compared with controls. This indicates that dietary haem increased colonic mucosal exposure to luminal irritants. Colonic epithelial proliferation was increased compared with controls (70 +/- 4 versus 48 +/- 8 d.p.m./microg DNA, P < 0.001). This was accompanied by metabolism of the ingested haem and solubilization of haem compounds in the faecal water. A high calcium diet largely prevented this metabolism and solubilization. It also inhibited the haem-induced cytolytic activity of faecal water and increase in faecal cation concentration. In accordance, the haem-induced colonic epithelial hyperproliferation was prevented. We therefore suggest that dietary calcium phosphate acts as a chemopreventive agent in colon carcinogenesis by inhibiting the cytolytic and hyperproliferative effects of dietary haem.
Autonomous Sampling of Water Columns Using Gliding Robotic Fish: Algorithms and Harmful-Algae-Sampling Experiments (2015)

Gliding robotic fish, which is a hybrid of underwater gliders and robotic fish, is energy efficient and highly maneuverable and holds strong promise for long-duration monitoring of underwater environments. In this paper, a novel scheme is proposed for autonomously sampling multiple water columns using gliding robotic fish. The scheme exploits energy-efficient spiral-down motion to sample each water column, followed by sagittal-plane glide-up toward the direction of the next water column. Once surfacing, the robot uses Global Positioning System guidance to reach the next column location through swimming. To enhance the path-tracking performance, a two-degree-of-freedom controller involving H <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">∞</sub> control is used in the spiral motion, and a sliding-mode controller is employed to regulate the yaw angle during glide-up. The sampling scheme has been implemented on a gliding robotic fish prototype, “Grace,” and verified first in pool experiments and then in field experiments involving the sampling of harmful algae concentration in the Wintergreen Lake, Michigan.
3T MRI-based estimation of scalar cochlear implant electrode position (2019)

Common techniques to evaluate intracochlear electrode position include ionised radiation by multi-slice computer tomography, digitalvolume tomography (MSCT, DVT) and flat panel tomography (FPT). Recent advances in the knowledge about handling MRI artefacts andthe pain-free performance of MRI scans in cochlear implantees showed that estimation of the intracochlear electrode position is possible at1.5 T with perimodiolar or midmodiolar arrays. The aim of the present study is to evaluate the assessment of the ipsilateral scalar positionof a cochlear implant lateral wall electrode by MRI sequences at 3T. In a prospective study we evaluated 10 patients implanted with a diametricallybipolar implant magnet system with a lateral wall electrode in the intrascalar electrode position in an axial and coronal positionand a T2 weighted sequence at 3T and a resolution of 0.8 mm. We compared the intracochlear position with routine postoperative DVTscan. In all cases, the MRT-estimated scalar position corresponded with that estimated by DVT scan. In all cases, a scala tympani positionwas present. While the position in the basal turn is reliably localisable, the first-turn visual assessment is difficult. Estimation of theintracochlear position of lateral wall cochlear implant electrodes by 3T MRI is possible for the basal turn. Electrode design plays a majorrole in visual assessment.
Reversible left ventricular dysfunction due to severe stenosis of the elephant trunk graft: A case report (2021)

Acquired coarctation of the aorta (CoA) following total aortic arch replacement (TAR) is a rare complication inducing left ventricular (LV) dysfunction probably due to increased LV afterload and secondary hypertension caused by increased upper body and decreased renal blood flow. We describe a case of a 35-year-old male who developed atypical CoA with severe LV dysfunction with LV ejection fraction of 10%, but without secondary hypertension after TAR using conventional elephant trunk (ET) technique for acute aortic dissection. Computed tomography revealed near-occlusive CoA due to narrowed distal ET. Because the myocardial histological findings were mild, and he had no cardiac failure history, we determined that LV function might be reversible. He underwent thoracic endovascular aortic repair (TEVAR), resulting in restored LV function. However, as the descending aortic false lumen distally to the end of ET was rapidly dilated, probably due to increased cardiac output and lower body blood flow, he underwent descending aortic replacement 3 months after TEVAR. In conclusion, a narrowed distal ET may cause LV dysfunction early after TAR, even without secondary hypertension. TEVAR may be a useful therapeutic option for a narrowed distant ET but can induce distal aortic dilatation. <<b>Learning objective:</b> A 35-year-old male demonstrated that acquired coarctation of the aorta due to a narrowed distant elephant trunk led to left ventricular (LV) dysfunction with comparable severity of dilated cardiomyopathy even with normal blood pressure. Thoracic endovascular aortic repair is an effective treatment option to restore LV function by decreasing LV afterload. However, a narrowed distal ET relief with an increased cardiac output might cause distal aortic dilatation.>.
New tools for mass isotopomer data evaluation in 13C flux analysis: Mass isotope correction, data consistency checking, and precursor relationships (2003)

13C metabolic flux analysis (MFA) is based on carbon-labeling experiments where a specifically (13)C labeled substrate is fed. The labeled carbon atoms distribute over the metabolic network and the label enrichment of certain metabolic pools is measured by using different methods. Recently, MS methods have been dramatically improved-large and precise datasets are now available. MS data has to be preprocessed and corrected for natural stable mass isotopes. In this article we present (1). a new elegant method to correct MS measurement data for natural stable mass isotopes by infinite dimensional matrix calculus and (2). we statistically analyze and discuss a reconstruction of labeling pattern in metabolic precursors from biosynthesis molecules. Moreover, we establish a new method for consistency checking of MS spectra that can be applied for automatic error recognition in high-throughput flux analysis procedures. Preprocessing the measurement data changes their statistical properties which have to be considered in the subsequent parameter fitting process for (13)C MFA. We show that correcting for stable mass isotopes leads to rather small correlations. On the other hand, a direct reconstruction of a precursor labeling pattern from an aromatic amino acid measurement turns out to be critical. Reasonable results are only obtained if additional, independent information about the labeling of at least one precursor is available. A versatile MatLab tool for the rapid correction and consistency checking of MS spectra is presented. Practical examples for the described methods are also given.
Mix & Latch: An Optimization Flow for High-Performance Designs With Single-Clock Mixed-Polarity Latches and Flip-Flops (2023)

Flip-flops are the most used sequential elements in synchronous circuits, but designs based on latches can operate at higher frequencies and occupy less area. Techniques to increase the maximum operating frequency of flip-flop based designs, such as time-borrowing, rely on tight hold constraints that are difficult to satisfy using traditional back-end optimization techniques. We propose Mix & Latch, a methodology to increase the operating frequency of synchronous digital circuits using a single clock tree and a mixed distribution of positive- and negative-edge-triggered flops, and positive- and negative-level-sensitive latches. An efficient mathematical model is proposed to optimize the type and location of the sequential elements of the circuit. We ensure that the initial registers are not moved from their initial location, although they may change type, thus allowing the use of equivalence checking and static timing analysis to verify formally the correctness of the transformation. The technique is validated using a <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$\mathrm {28 \text {n} \text {m} }$ </tex-math></inline-formula> CMOS FDSOI technology, obtaining <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$\mathrm {1.33 X}$ </tex-math></inline-formula> post-layout average operating frequency improvement on a broad set of benchmarks over a standard commercial design flow. Additionally, the circuit area was also reduced by more than <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$\mathrm {1.19 X}$ </tex-math></inline-formula> on average for the same benchmarks, although the overall area reduction is not a goal of the optimization algorithm. To the best of our knowledge, this is the first work that proposes combining mixed-polarity flip-flops and latches to improve the circuit performance.
Survival in Dementia and Cognitive Impairment Not Dementia: 16 Year Follow Up from the ACCORD Study (P1.102) (2016)

Objective: Examine survival and risk factor effects in a cohort of cognitive impairment not dementia (CIND) and dementia. Compare survival to general population in British Columbia (BC). Background: Estimates of survival are integral to the care of patients diagnosed with dementia. Few Canadian studies have long-term follow-up of well-described cohorts, analyzing survival with multiple risk factors. Design/Methods: We studied survival at a single ACCORD center site. 218 patients diagnosed with CIND or dementia followed from recruitment between 1997-1999. Vital status completed for all patients on censor date (June 20, 2015). Risk factors including age, sex, education, MMSE, CIRS, NPI, FRS, DAD, Hachinski, vascular risk factors, APOE4, and AchEI use evaluated in AD and Other Dementias (OD) subgroups using Kaplan-Meier and Cox regression. Survival compared to age-matched life expectancy in BC. Results: Overall 183 (84[percnt]) deaths observed over 16.6 years mean follow up. 16/39 (41[percnt]) CIND died; 136/144 (94[percnt]) AD died; 31/35 (89[percnt]) OD died (median survival for dementia groups: 7.1 years). Given the heterogeneity and small sample size of CIND, effects of risk factors were evaluated only in patients with dementia. Survival times did not vary between AD and OD (p=0.53). Shorter survival was associated with age, DAD scores <55[percnt] (HR 1.92, 95[percnt]CI 1.20-3.08) and CIRS scores >7 (HR 1.90, 95[percnt]CI 1.23-2.93); the latter two remained significant after adjustment. No significant effect was observed with other variables. Compared to BC population, decrease of life expectancy for dementia subjects aged 65-69 was 11.35 years and 1.82 years for ≥80. Conclusions: Survival with dementia is shorter than population life expectancies for each age strata, with greatest impact in younger patients. Cumulative medical illness and functional disabilities are the most significant predictors of survival and can guide prognosis. ACCORD funded by Canada’s Medical Research Council (now CIHR) and Pharmaceutical Manufacturers’ Association of Canada.
Plant microbiomes harbor potential to promote nutrient turnover in impoverished substrates of a Brazilian biodiversity hotspot (2022)

The substrates of the Brazilian campos rupestres, a grassland ecosystem, have extremely low concentrations of phosphorus and nitrogen, imposing restrictions to plant growth. Despite that, this ecosystem harbors almost 15% of the Brazilian plant diversity, raising the question of how plants acquire nutrients in such a harsh environment. Here, we set out to uncover the taxonomic profile, the compositional and functional differences and similarities, and the nutrient turnover potential of microbial communities associated with two plant species of the campos rupestres-dominant family Velloziaceae that grow over distinct substrates (soil and rock). Using amplicon sequencing data, we show that, despite the pronounced composition differentiation, the plant-associated soil and rock communities share a core of highly efficient colonizers that tend to be highly abundant and is enriched in 21 bacterial families. Functional investigation of metagenomes and 522 metagenome-assembled genomes revealed that the microorganisms found associated to plant roots are enriched in genes involved in organic compound intake, and phosphorus and nitrogen turnover. We show that potential for phosphorus transport, mineralization, and solubilization are mostly found within bacterial families of the shared microbiome, such as Xanthobacteraceae and Bryobacteraceae. We also detected the full repertoire of nitrogen cycle-related genes and discovered a lineage of Isosphaeraceae that acquired nitrogen-fixing potential via horizontal gene transfer and might be also involved in nitrification via a metabolic handoff association with Binataceae. We highlight that plant-associated microbial populations in the campos rupestres harbor a genetic repertoire with potential to increase nutrient availability and that the microbiomes of biodiversity hotspots can reveal novel mechanisms of nutrient turnover.
A Man with Fever, Cough, and Rash (2014)

A 67-year-old man presented to the emergency department with a 5-week history of recurrent daily fevers, with temperatures as high as 38.7°C, night sweats, dyspnea, and cough. He reported no dysuria, chills, diarrhea, or vomiting. During the preceding year, he had had no known contact with persons who were sick, and had not traveled outside the United States. In the preceding . . .
INFLUENCE OF ENDURANCE EXERCISE ON THE RISK OF PNEUMONIA AND FEVER IN LEUKEMIA AND LYMPHOMA PATIENTS UNDERGOING HIGH DOSE CHEMOTHERAPY. A PILOT STUDY (2012)

Pneumonia and fever are common side effects of high dose chemotherapy (HDC). The positive influence of physical activity on physiological and psychological parameters in cancer patients has been demonstrated in several studies. In this non-randomized controlled pilot study we investigated the infection and pneumonia risk in 36 high dose chemotherapy patients undergoing a supervised endurance exercise program. 18 patients exercised for at least 3 weeks, starting with initiation of chemotherapy. These patients in the intervention group were compared with 18 patients who were matched by disease (leukemia/lymphoma), sex, age, risk factors, therapy protocols and did not take part in the exercise intervention. Leukemia and lymphoma groups were evaluated separately. In the leukemia group significant higher pneumonia rates could be observed in the control group (p = 0.040) when compared to the intervention group. Further an almost significantly higher risk (p = 0.061) of developing a pneumonia and fever was detected in the control group. In this pilot study, we gained first important positive experiences in possibly preventing pneumonias and fever through endurance training. Due to the non-randomized study design and small sample size the results are limited yet not irrelevant. RCTs with larger sample sizes are necessary to prove these findings
Safety and Efficacy of Long‐Term Voclosporin Treatment for Lupus Nephritis in the Phase 3 AURORA 2 Clinical Trial (2023)

Data demonstrate the safety and efficacy of long-term voclosporin treatment over three years of follow-up in patients with LN.
Shape completion enabled robotic grasping (2017)

This work provides an architecture to enable robotic grasp planning via shape completion. Shape completion is accomplished through the use of a 3D convolutional neural network (CNN). The network is trained on our own new open source dataset of over 440,000 3D exemplars captured from varying viewpoints. At runtime, a 2.5D pointcloud captured from a single point of view is fed into the CNN, which fills in the occluded regions of the scene, allowing grasps to be planned and executed on the completed object. Runtime shape completion is very rapid because most of the computational costs of shape completion are borne during offline training. We explore how the quality of completions vary based on several factors. These include whether or not the object being completed existed in the training data and how many object models were used to train the network. We also look at the ability of the network to generalize to novel objects allowing the system to complete previously unseen objects at runtime. Finally, experimentation is done both in simulation and on actual robotic hardware to explore the relationship between completion quality and the utility of the completed mesh model for grasping.
A new suffix tree similarity measure for document clustering (2007)

In this paper, we propose a new similarity measure to compute the pairwise similarity of text-based documents based on suffix tree document model. By applying the new suffix tree similarity measure in Group-average Agglomerative Hierarchical Clustering (GAHC) algorithm, we developed a new suffix tree document clustering algorithm (NSTC). Experimental results on two standard document clustering benchmark corpus OHSUMED and RCV1 indicate that the new clustering algorithm is a very effective document clustering algorithm. Comparing with the results of traditional word term weight tf-idf similarity measure in the same GAHC algorithm, NSTC achieved an improvement of 51% on the average of F-measure score. Furthermore, we apply the new clustering algorithm in analyzing the Web documents in online forum communities. A topic oriented clustering algorithm is developed to help people in assessing, classifying and searching the the Web documents in a large forum community.
Prostaglandin E2, thromboxane B2, and leukotriene B4 release from peritoneal macrophages by different osmotic agents in nonuremic guinea pigs. (1989)

Interleukin-1 (Il-1), prostaglandins, and leukotrienes have been identified as inflammatory parameters in the setting of peritoneal dialysis. Recently, it was postulated that chronic overstimulation of peritoneal macrophages (PM) may result in fibrosis and loss of ultrafiltration. The aim of the present study was to investigate whether alternative osmotic agents (polyglucose, amino acids, glycerol, bicarbonate/glucose, gelatine, hydroxyethyl starch) provoke greater eicosanoid release by PMs than glucose. Fifty milliliters of sterile dialysate containing different osmotic agents were injected intraperitoneally into nonuremic guinea pigs. After 4 hours of dwell time, prostaglandin E2 (PGE2), thromboxane B2 (TXB2), and leukotriene B4 (LTB4) production was analyzed in peritoneal effluents using specific radioimmunoassays (RIA) after liquid extraction. Cyclooxygenase products were generated with all osmotic agents: PGE2 concentrations ranged from 0.9 to 2.8 ng/4h, and TXB2 levels ranged from 39 to 49 ng/4h. In addition, the lipoxygenase product LTB4 was found in concentrations between 1.8 and 3.5 ng/4h. There were no significant differences in eicosanoid release among the osmotic agents. Thus, in this experimental setting, the capacity of PM to release inflammatory mediators did not correlate with the chemical composition of the dialysis solutions.
Optimization of the optical array geometry for IceCube-Gen2 (2021)

IceCube-Gen2 is a planned extension of the IceCube Neutrino Observatory at the South Pole designed to study the high-energy neutrino sky from TeV to EeV energies with a five times better point source sensitivity than the current IceCube detector. This is achieved by deploying 120 new strings with attached optical sensors in a pattern around IceCube that features considerably larger distances between individual strings than the ~125 m for the existing detector. Here, we present the results of an optimization study searching for the best point source sensitivity while varying the IceCube-Gen2 string spacing between 150 m and 350 m.
A General [3 + 2 + 1] Annulation Strategy for the Preparation of Pyridine N-Oxides (2000)

[figure: see text] Stabilized ketone, aldehyde, and ester enolates react with vinamidinium hexafluorophosphate salts and hydroxylamine hydrochloride to give access to the corresponding pyridine N-oxides. The annulation reactions proceed in good to excellent yields with vinamidinium salts with a range of beta-substituents (R3 = halo, aryl, nitro, trifluoromethyl).