Miracle-dz/UniFAR-FTUs huggingface dataset:
Links between complexity theory and constrained block coding

The goal of this paper is to establish links between computational complexity theory and the theory and practice of constrained block coding. The complexities of several fundamental problems in constrained block coding are shown to be complete in various classes of the existing complexity-theoretic structure. The results include (relatively rare) /spl Sigma//sub 2//sup p/-, /spl Sigma//sub 3//sup p/, and NP/sup PP/-completeness results. Two types of problems are considered: (1) the problem of designing encoder and decoder circuits using minimum or approximately minimum hardware for a given constraint and a given rate; (2) computing the maximum rate of a block code for a given constraint and codeword length. In both cases, a constraint is specified by a deterministic finite state transition diagram. Another question studied is whether maximum-rate block codes can always be implemented by encoders and decoders of polynomial size. The answer to this question is shown to be closely related to the complexity of PP.
Nutrition Screening vs Nutrition Assessment: What’s the Difference?

Screening and assessment imply different processes, with the former indicating risk factors for a deprived nutrition condition and the latter providing the nutrition diagnosis. Both should be routinely performed at hospital admission according to recommended guidelines; however, this is not the reality worldwide, and undernutrition remains highly prevalent in the hospital setting. Therefore, the objective of the current review is to delve into the principles leading to nutrition status deficiencies and how they should be addressed by screening and assessment. A critical appraisal for the reasons associated with the misunderstanding between screening and assessing is proposed without further discussing the many available screening tools while approaching some of the assessment instruments.
Soil organic carbon saturation deficit under primary agricultural managements across major croplands in China

ABSTRACT Introduction: To generate information for the effective management of soil organic carbon (SOC) sequestration in Chinese croplands, we compared the additional organic carbon (C) that can be stabilized by fine soil particles (<20 μm) with typical fertilization practices across soil types and climate zones. Using data from 30 long-term experimental study sites across the major agricultural zones in China, we estimated stable SOC saturation deficit (SOCdeficit) under no fertilization (CK), chemical fertilization (CF), straw plus CF (S + CF), and manure plus CF (M + CF). Stable SOCdeficit was defined as the difference between potential and current SOC stabilized by fine soil particles. Outcomes: Stable SOCdeficit values varied from 51% to 82%. Soils dominated by 2:1 clay minerals showed larger stable SOCdeficit than soils dominated by 1:1 clay minerals under each treatment. For soils dominated by 2:1 clay minerals, stable SOCdeficit was significantly lower under M + CF (69%) than under CK, CF, and S + CF (78–82%) treatments, and it increased with increasing mean annual temperature (<10°C). In soils dominated by 1:1 clay minerals, stable SOCdeficit was considerably lower in paddy and paddy-upland than in upland soils, suggesting that paddies effectively stabilize C inputs. Discussion: Agricultural soils in China have considerable C sequestration potential, despite decades of fertilization practices. To manage soil C sequestration and model soil C dynamics effectively, factors such as soil mineral types, fertilization, and cropland use should be considered. Conclusion: Our results demonstrated that manure addition was the best fertilization method for improving soil fertility, whereas straw return in Chinese croplands should take into account climate mitigation in future.
The 2001 trading agent competition

The 2001 Trading Agent Competition was the second in a series of events aiming to shed light on research issues in automating trading strategies. Based on a challenging market scenario in the domain of travel shopping, the competition presents agents with difficult issues in bidding strategy, market prediction, and resource allocation. Entrants in 2001 demonstrated substantial progress over the prior year, with the overall level of competence exhibited suggesting that trading in online markets is a viable domain for highly autonomous agents.
Retinoic acid and chick limb bud development.

The chick limb bud is a powerful experimental system in which to study pattern formation in vertebrate embryos. Exogenously applied retinoic acid, a vitamin A derivative, can bring about changes in pattern and, on several grounds, is a good candidate for an endogenous morphogen. As such, the local concentration of retinoic acid might provide cells with information about their position in relation to one axis of the limb. Alternatively, retinoic acid may be part of a more complex signalling system. Homeobox genes are possible target genes for regulation by retinoic acid in the limb. In particular, one homeobox gene, XlHbox 1 is expressed locally in the mesenchyme of vertebrate forelimbs and might code for an anterior position. When the pattern of the chick wing is changed by retinoic acid or by grafts of signalling tissue such that anterior cells now form posterior structures, the domain of XlHbox 1 expression expands rather than contracts. The expansion of XlHbox 1 expression correlates with shoulder girdle abnormalities. Retinoic acid application leads to visible changes in bud shape and this allows dissection of the way in which patterning is co-ordinated with morphogenesis. Results of recombination experiments and studies of changes in the apical ridge and proliferation in the mesenchyme suggest the following scheme: retinoic acid is involved in specification of position of mesenchyme cells; this specification determines their local interaction with the ridge that controls ridge morphology; the thickened apical ridge permits local proliferation in the underlying mesenchyme. (ABSTRACT TRUNCATED AT 250 WORDS)
Evaluation of Simplified Polarimetric Decomposition for Soil Moisture Retrieval over Vegetated Agricultural Fields

This paper investigates a simplified polarimetric decomposition for soil moisture retrieval over agricultural fields. In order to overcome the coherent superposition of the backscattering contributions from vegetation and underlying soils, a simplification of an existing polarimetric decomposition is proposed in this study. It aims to retrieve the soil moisture by using only the surface scattering component, once the volume scattering contribution is removed. Evaluation of the proposed simplified algorithm is performed using extensive ground measurements of soil and vegetation characteristics and the time series of UAVSAR (Uninhabited Aerial Vehicle Synthetic Aperture Radar) data collected in the framework of SMAP (Soil Moisture Active Passive) Validation Experiment 2012 (SMAPVEX12). The retrieval process is tested and analyzed in detail for a variety of crops during the phenological stages considered in this study. The results show that the performance of soil moisture retrieval depends on both the crop types and the crop phenological stage. Soybean and pasture fields present the higher inversion rate during the considered phenological stage, while over canola and wheat fields, the soil moisture can be retrieved only partially during the crop developing stage. RMSE of 0.06–0.12 m3/m3 and an inversion rate of 26%–38% are obtained for the soil moisture retrieval based on the simplified polarimetric decomposition.
Protein Carbonyl, But Not Malondialdehyde, Is Associated With ICU Mortality in Patients With Septic Shock

Background: The objective of our study was to evaluate the association of serum malondialdehyde (MDA) and protein carbonyl concentration with intensive care unit (ICU) mortality in patients with septic shock. Methods: We prospectively evaluated 175 patients aged over 18 years with septic shock upon ICU admission. However, 16 patients were excluded. Thus, 159 patients were enrolled in the study. In addition, we evaluated 16 control patients. At the time of the patients’ enrollment, demographic information was recorded. Blood samples were taken within the first 24 hours of the patient’s admission to determine serum MDA and protein carbonyl concentrations. Results: The mean age was 67.3 ± 15.9 years, 44% were males, and the ICU mortality rate was 67.9%. Median MDA concentration was 1.53 (0.83-2.22) µmol/L, and median protein carbonyl concentration was 24.0 (12.7-32.8) nmol/mL. Patients who died during ICU stay had higher protein carbonyl concentration. However, there was no difference in MDA levels between these patients. Receiver operating characteristic curve analysis showed that higher levels of protein carbonyl were associated with ICU mortality (area under the curve: 0.955; 95% confidence interval [CI]: 0.918-0.992; P < .001) at the cutoff of >22.83 nmol/mL (sensibility: 80.4% and specificity: 98.1%). In the logistic regression models, protein carbonyl concentrations (odds ratio [OR]: 1.424; 95% CI: 1.268-1.600; P < .001), but not MDA concentrations (OR: 1.087; 95% CI: 0.805-1.467; P = .59), were associated with ICU mortality when adjusted for age, gender, and Acute Physiology and Chronic Health Evaluation (APACHE) II score; and when adjusted by APACHE II score, lactate, and urea; protein carbonyl concentrations (OR: 1.394; 95% CI: 1.242-1.564; P < .001); and MDA (OR: 1.054; 95% CI: 0.776-1.432; P = .73). Conclusion: In conclusion, protein carbonyl, but not MDA, concentration is associated with ICU mortality in patients with septic shock.
Adaptive Memory

Recent studies suggest that human memory systems are “tuned” to remember information that is processed in terms of its fitness value. When people are asked to rate the relevance of words to a survival scenario, performance on subsequent surprise memory tests exceeds that obtained after most other known encoding techniques. The present experiments explored this effect using survival scenarios designed to mimic the division of labor thought to characterize early hunter-gatherer societies. It has been suggested that males and females have different cognitive specializations due to the unique survival tasks (hunting and gathering, respectively) they typically performed during periods of human evolution; the present experiments tested whether such specializations might be apparent in memory for words rated for relevance to these activities. Males and females were asked to rate the relevance of random words to prototypical hunting and gathering scenarios or to matched, non-fitness-relevant control scenarios (gathering food on a scavenger hunt or in a hunting contest). Surprise retention tests revealed superior memory for the words when they were rated for relevance to hunting and gathering scenarios, compared with when they were rated for relevance to the control scenarios, but no sex differences were found in memory performance.
CTL0511 from Chlamydia trachomatis Is a Type 2C Protein Phosphatase with Broad Substrate Specificity

ABSTRACT Protein phosphorylation has become increasingly recognized for its role in regulating bacterial physiology and virulence. Chlamydia spp. encode two validated Hanks'-type Ser/Thr protein kinases, which typically function with cognate protein phosphatases and appear capable of global protein phosphorylation. Consequently, we sought to identify a Ser/Thr protein phosphatase partner for the chlamydial kinases. CTL0511 from Chlamydia trachomatis L2 434/Bu, which has homologs in all sequenced Chlamydia spp. , is a predicted type 2C Ser/Thr protein phosphatase (PP2C). Recombinant maltose-binding protein (MBP)-tagged CTL0511 (rCTL0511) hydrolyzed p-nitrophenyl phosphate (pNPP), a generic phosphatase substrate, in a MnCl2-dependent manner at physiological pH. Assays using phosphopeptide substrates revealed that rCTL0511 can dephosphorylate phosphorylated serine (P-Ser), P-Thr, and P-Tyr residues using either MnCl2 or MgCl2, indicating that metal usage can alter substrate preference. Phosphatase activity was unaffected by PP1, PP2A, and PP3 phosphatase inhibitors, while mutation of conserved PP2C residues significantly inhibited activity. Finally, phosphatase activity was detected in elementary body (EB) and reticulate body (RB) lysates, supporting a role for protein dephosphorylation in chlamydial development. These findings support that CTL0511 is a metal-dependent protein phosphatase with broad substrate specificity, substantiating a reversible phosphorylation network in C. trachomatis. IMPORTANCE Chlamydia spp. are obligate intracellular bacterial pathogens responsible for a variety of diseases in humans and economically important animal species. Our work demonstrates that Chlamydia spp. produce a PP2C capable of dephosphorylating P-Thr, P-Ser, and P-Tyr and that Chlamydia trachomatis EBs and RBs possess phosphatase activity. In conjunction with the chlamydial Hanks'-type kinases Pkn1 and PknD, validation of CTL0511 fulfills the enzymatic requirements for a reversible phosphoprotein network. As protein phosphorylation regulates important cellular processes, including metabolism, differentiation, and virulence, in other bacterial pathogens, these results set the stage for elucidating the role of global protein phosphorylation in chlamydial physiology and virulence.
Gastric Cancer: Descriptive Epidemiology, Risk Factors, Screening, and Prevention

Less than a century ago, gastric cancer was the most common cancer in the United States and perhaps throughout the world. Despite its worldwide decline in incidence over the past century, gastric cancer remains a major killer across the globe. This article reviews the epidemiology, screening, and prevention of gastric cancer. We first discuss the descriptive epidemiology of gastric cancer, including its incidence, survival, mortality, and trends over time. Next, we characterize the risk factors for gastric cancer, both environmental and genetic. Serologic markers and histological precursor lesions of gastric cancer and early detection of gastric cancer using these markers are reviewed. Finally, we discuss prevention strategies and provide suggestions for further research. Cancer Epidemiol Biomarkers Prev; 23(5); 700–13. ©2014 AACR.
Technical Developments and Clinical Use of Telemedicine in Sleep Medicine

The use of assistive technology and telemedicine is likely to continue to shape our medical practice in the future, notably in the field of sleep medicine, especially within developed countries. Currently, the number of people suffering from obstructive sleep apnea syndrome (OSAS) is increasing. Telemedicine (TM) can be used in a variety of ways in sleep medicine: telediagnostics, teleconsultation, teletherapy and telemonitoring of patients being treated with positive pressure devices. In this review, we aim to summarize the recent scientific progresses of these techniques and their potential clinical applications and give consideration to the remaining problems related to TM application.
Short-term complications after colic surgery in geriatric versus mature non-geriatric horses.

OBJECTIVE To compare in geriatric and mature horses the occurrence of short-term complications and short-term outcome associated with complications after colic surgery. STUDY DESIGN Retrospective case-control study. SAMPLE POPULATION Horses aged ≥20 years (geriatric, n = 78) and 4-15 years (mature non-geriatric, n = 156) that had exploratory celiotomy for colic and survived recovery from general anesthesia. METHODS Medical records (2000-2010) of horses that recovered from general anesthesia after colic surgery were reviewed. Postoperative complications evaluated included postoperative reflux (POR), diarrhea, inappetence, fever, leukopenia, incisional infection, incisional dehiscence, thrombophlebitis, colic, repeat celiotomy, pneumonia, and laminitis. Short-term outcome (alive vs. dead at hospital discharge) of geriatric and mature horses with these complications were compared. Data were analyzed using a χ(2) or Fisher's exact test or an ANOVA. Level of significance P < . 05. RESULTS Geriatric horses had higher odds of having a small intestinal strangulating lesion than mature horses. A higher proportion of geriatric horses had POR and inappetence; however, there was no difference in the proportion of geriatric and mature horses with small intestinal strangulating lesions having POR. Short-term outcome with and without complications was similar between the 2 age groups. CONCLUSION Geriatric and mature horses have similar occurrences of short-term complications and short-term outcomes associated with complications after colic surgery.
Age-Related Adaptation of Bone-PDL-Tooth Complex: Rattus-Norvegicus as a Model System

Functional loads on an organ induce tissue adaptations by converting mechanical energy into chemical energy at a cell-level. The transducing capacity of cells alters physico-chemical properties of tissues, developing a positive feedback commonly recognized as the form-function relationship. In this study, organ and tissue adaptations were mapped in the bone-tooth complex by identifying and correlating biomolecular expressions to physico-chemical properties in rats from 1.5 to 15 months. However, future research using hard and soft chow over relevant age groups would decouple the function related effects from aging affects. Progressive curvature in the distal root with increased root resorption was observed using micro X-ray computed tomography. Resorption was correlated to the increased activity of multinucleated osteoclasts on the distal side of the molars until 6 months using tartrate resistant acid phosphatase (TRAP). Interestingly, mononucleated TRAP positive cells within PDL vasculature were observed in older rats. Higher levels of glycosaminoglycans were identified at PDL-bone and PDL-cementum entheses using alcian blue stain. Decreasing biochemical gradients from coronal to apical zones, specifically biomolecules that can induce osteogenic (biglycan) and fibrogenic (fibromodulin, decorin) phenotypes, and PDL-specific negative regulator of mineralization (asporin) were observed using immunohistochemistry. Heterogeneous distribution of Ca and P in alveolar bone, and relatively lower contents at the entheses, were observed using energy dispersive X-ray analysis. No correlation between age and microhardness of alveolar bone (0.7±0.1 to 0.9±0.2 GPa) and cementum (0.6±0.1 to 0.8±0.3 GPa) was observed using a microindenter. However, hardness of cementum and alveolar bone at any given age were significantly different (P<0.05). These observations should be taken into account as baseline parameters, during development (1.5 to 4 months), growth (4 to 10 months), followed by a senescent phase (10 to 15 months), from which deviations due to experimentally induced perturbations can be effectively investigated.
Differential Specificity of Human and Escherichia coli Endonuclease III and VIII Homologues for Oxidative Base Lesions*

In human cells, oxidative pyrimidine lesions are restored by the base excision repair pathway initiated by homologues of Endo III (hNTH1) and Endo VIII (hNEIL1 and hNEIL2). In this study we have quantitatively analyzed and compared their activity toward nine oxidative base lesions and an apurinic/apyrimidinic (AP) site using defined oligonucleotide substrates. hNTH1 and hNEIL1 but not hNEIL2 excised the two stereoisomers of thymine glycol (5R-Tg and 5S-Tg), but their isomer specificity was markedly different: the relative activity for 5R-Tg:5S-Tg was 13:1 for hNTH1 and 1.5:1 for hNEIL1. This was also the case for their Escherichia coli homologues: the relative activity for 5R-Tg:5S-Tg was 1:2.5 for Endo III and 3.2:1 for Endo VIII. Among other tested lesions for hNTH1, an AP site was a significantly better substrate than urea, 5-hydroxyuracil (hoU), and guanine-derived formamidopyrimidine (mFapyG), whereas for hNEIL1 these base lesions and an AP site were comparable substrates. In contrast, hNEIL2 recognized an AP site exclusively, and the activity for hoU and mFapyG was marginal. hNEIL1, hNEIL2, and Endo VIII but not hNTH1 and Endo III formed cross-links to oxanine, suggesting conservation of the -fold of the active site of the Endo VIII homologues. The profiles of the excision of the Tg isomers with HeLa and E. coli cell extracts closely resembled those of hNTH1 and Endo III, confirming their major contribution to the repair of Tg isomers in cells. However, detailed analysis of the cellular activity suggests that hNEIL1 has a significant role in the repair of 5S-Tg in human cells.
Nitrogen Cycling in Permeable Sediments: Process-based Models for Streams and the Coastal Ocean - eScholarship

Bioavailable forms of nitrogen, such as nitrate, are necessary for aquatic ecosystem productivity. Excess nitrate in aquatic systems, however, can adversely affect ecosystems and degrade both surface water and groundwater. Some of this excess nitrate can be removed in the sediments that line the bottom of rivers and coastal waters, through the exchange of water between surface water and groundwater (known as hyporheic exchange). Several process-based models have been proposed for estimating nitrate removal in aquatic systems but these (1) do not consider the multiscale nature of hyporheic exchange flows; (2) rely on simplified conceptualizations of mixing within streambed sediments (e.g., a well-mixed box); (3) neglect important steps in the N-cycle (e.g., nitrification and ammonification); and/or (4) adopt pseudo-first-order kinetic descriptions of denitrification. On the other hand, a number of empirical correlations have been published based on in-stream measurements of nitrate uptake using reach-scale stable isotope tracer experiments. While these correlations are noteworthy in many respects, they do not account for physical processes known to play an important role in nutrient processing, such as the exchange of water between a stream, sediments, and groundwater.In this thesis, I develop and test a simple and scalable process-based model for estimating the nitrate uptake velocity that addresses the limitations identified above. In particular, my model accounts for: (1) hyporheic exchange at multiple scales together with ambient groundwater flow; (2) the broad residence time distributions characteristic of hyporheic exchange; (3) key biogeochemical reactions associated with N-cycling, including respiration, ammonification, nitrification, and denitrification; and (4) the nonlinear nature of the pertinent biogeochemical reaction rates, including Monod kinetics for aerobic respiration and denitrification, and second-order kinetics for nitrification. Using this modeling framework I systematically evaluate primary controls on stream N-cycling and evaluate how multi-scale and regional factors are likely to affect this process. I also demonstrate how my model predictions compare with previously published reach-scale measurements of nitrate removal, develop scaling relationships by which my process-based model can be applicable to larger scales (i.e., watershed and regional scales), and provide some mechanistic explanations for previous observations.
Studies with the maximal histamine test.

EDITORIAL SYNOPSIS The maximal acid output in Indian controls and subjects with duodenal ulcer is lower than that reported from the West. There is a significantly higher acid output in men than in women of comparable age and weight groups. After 50 years of age, there is a falling-off in acid output in both sexes. No significant decline in acid outputs could be established with age in subjects under 50 years of age. There is an increase in acid output with increase in weight in both sexes, more pronounced for females. Male smokers have a higher acid output than men who do not smoke, but the difference is not significant. There is no difference in acid output between vegetarians and non-vegetarians.