Miracle-dz/UniFAR-FTUs huggingface dataset:
The neonatal bowel microbiome in health and infection

Purpose of review In newborns, interactions between the host and the microbiome operate synergistically, modulating host immune function and shaping the microbiome. Next generation molecular sequencing methodologies in tandem with modeling complex communities allow insights into the role of the microbiome in health and disease states. Infection-related disease states in which dysbiosis is integral include late-onset sepsis (LOS) and necrotizing enterocolitis (NEC), which still cause deaths and morbidity. Understanding microbiomic interactions may lead to alternative prevention, monitoring or treatment strategies, and modulation of long-term health outcomes especially in the preterm population. Recent studies have advanced understanding of the microbiome in NEC and LOS. Recent findings Mechanisms of host–microbiome interaction have been demonstrated. Patterns of microbiomic change in association with NEC and LOS have been observed, with community changes dominated by Proteobacteria and Firmicutes appearing to precede NEC, and very early microbiomic signatures influencing LOS. Data on viral and fungal elements are emerging. Summary Greater understanding of the neonatal bowel microbiome may allow tailored clinical practice and therapeutic intervention. Data handling and interpretation is challenging. Mechanistic studies of clinical interventions that affect the gut microbiome are important next steps.
Adaptive linear step-up procedures that control the false discovery rate

The linear step-up multiple testing procedure controls the false discovery rate at the desired level q for independent and positively dependent test statistics. When all null hypotheses are true, and the test statistics are independent and continuous, the bound is sharp. When some of the null hypotheses are not true, the procedure is conservative by a factor which is the proportion m-sub-0/m of the true null hypotheses among the hypotheses. We provide a new two-stage procedure in which the linear step-up procedure is used in stage one to estimate m-sub-0, providing a new level q′ which is used in the linear step-up procedure in the second stage. We prove that a general form of the two-stage procedure controls the false discovery rate at the desired level q. This framework enables us to study analytically the properties of other procedures that exist in the literature. A simulation study is presented that shows that two-stage adaptive procedures improve in power over the original procedure, mainly because they provide tighter control of the false discovery rate. We further study the performance of the current suggestions, some variations of the procedures, and previous suggestions, in the case where the test statistics are positively dependent, a case for which the original procedure controls the false discovery rate. In the setting studied here the newly proposed two-stage procedure is the only one that controls the false discovery rate. The procedures are illustrated with two examples of biological importance. Copyright 2006, Oxford University Press.
Strontium Ranelate Increases Cartilage Matrix Formation

Based on previous studies showing that strontium ranelate (S12911) modulates bone loss in osteoporosis, it could be hypothesized that this drug also is effective on cartilage degradation in osteoarthritis (OA). This was investigated in vitro on normal and OA human chondrocytes treated or not treated with interleukin‐1β (IL‐1β). This model mimics, in vitro, the imbalance between chondroformation and chondroresorption processes observed in vivo in OA cartilage. Chondrocytes were isolated from cartilage by enzymatic digestion and cultured for 24–72 h with 10−4−10−3 M strontium ranelate, 10−3 M calcium ranelate, or 2 · 10−3 M SrCl2 with or without IL‐1β or insulin‐like growth factor I (IGF‐I). Stromelysin activity and stromelysin quantitation were assayed by spectrofluorometry and enzyme amplified sensitivity immunoassay (EASIA), respectively. Proteoglycans (PG) were quantified using a radioimmunoassay. Newly synthesized glycosaminoglycans (GAGs) were quantified by labeled sulfate (Na235SO4) incorporation. This method allowed the PG size after exclusion chromatography to be determined. Strontium ranelate, calcium ranelate, and SrCl2 did not modify stromelysin synthesis even in the presence of IL‐1β. Calcium ranelate induced stromelysin activation whereas strontium compounds were ineffective. Strontium ranelate and SrCl2 both strongly stimulated PG production suggesting an ionic effect of strontium independent of the organic moiety. Moreover, 10−3 M strontium ranelate increased the stimulatory effect of IGF‐I (10−9 M) on PG synthesis but did not reverse the inhibitory effect of IL‐1β. Strontium ranelate strongly stimulates human cartilage matrix formation in vitro by a direct ionic effect without stimulating the chondroresorption processes. This finding provides a preclinical basis for in vivo testing of strontium ranelate in OA.
Antenna diversity measurement system in anechoic chamber

This paper presents theoretical and experimental results to demonstrate the capabilities of an antenna-diversity measurement set-up installed in an anechoic chamber. A numerical model of the set-up has been developped and provides theoretical results on the accuracy and limitations of the system. Experimental tests have been performed with dipole antennas in space-diversity with good agreement with the simulations.
Prevalence of Catatonia and Its Moderators in Clinical Samples: Results from a Meta-analysis and Meta-regression Analysis

Catatonia is an independent syndrome that co-occurs with several mental and medical conditions. We performed a systematic literature review in PubMed/Scopus until February 2017 and meta-analyzed studies reporting catatonia prevalence. Across 74 studies (cross-sectional = 32, longitudinal = 26, retrospective = 16) providing data collected from 1935 to 2017 across all continents, mean catatonia prevalence was 9.0% (k = 80, n = 110764; 95% CI = 6.9-11.7, I2 = 98%, publication bias P < .01), decreasing to 7.8% (k = 19, n = 7612, 95% CI = 7-8.7, I2 = 38.9%) in a subgroup with low heterogeneity. Catatonia prevalence was 23.9% (k = 8, n = 1168, 95% CI = 10-46.9, I2 = 96%) in patients undergoing ECT/having elevated creatinine phosphokinase. Excluding ECT samples, the catatonia prevalence was 8.1% (k = 72, n = 109606, 95% CI = 6.1-10.5, I2 = 98%, publication bias P < .01), with sensitivity analyses demonstrating that country of study origin (P < .001), treatment setting (P = .003), main underlying condition (P < .001), and sample size (P < .001)moderated catatonia prevalence, being highest in Uganda (48.5%, k = 1) and lowest in Mexico (1.9%, 95% CI = 0.4-8.8, I2 = 67%, k = 2), highest in nonpsychiatric out- or inpatient services (15.8%, 95% CI = 8.1-28.4, I2 = 97%, k = 15)and lowest in psychiatric outpatients services (3.2%, 95% CI = 1.7-6.1, I2 = 50%, k = 3), highest in presence of medical or neurological illness with no comorbid psychiatric condition (20.6%, 95% CI = 11.5-34.2, I2 = 95%, k = 10)and lowest in mixed psychiatric samples (5.7%, 95% CI = 4.2-7.7, I2 =98%, k = 43), highest in studies with sample sizes <100 (20.7%, 95% CI = 12.8-31.6, I2 = 90%, k = 17) and lowest in studies with sample sizes >1000 (2.3%, 95% CI = 1.3-3.9, I2 = 99%, k = 16). Meta-regression showed that smaller sample size (P < .01) and less major depressive disorder (P = .02) moderated higher catatonia prevalence. Year of data collection did not significantly moderate the results. Results from this first meta-analysis of catatonia frequencies across time and disorders suggest that catatonia is an epidemiologically and clinically relevant condition that occurs throughout several mental and medical conditions, whose prevalence has not decreased over time and does not seem to depend on different rating scales/criteria. However, results were highly heterogeneous, calling for a cautious interpretation.
Fast k-means with accurate bounds

We propose a novel accelerated exact k-means algorithm, which performs better than the current state-of-the-art low-dimensional algorithm in 18 of 22 experiments, running up to 3 times faster. We also propose a general improvement of existing state-of-the-art accelerated exact k-means algorithms through better estimates of the distance bounds used to reduce the number of distance calculations, and get a speedup in 36 of 44 experiments, up to 1.8 times faster. We have conducted experiments with our own implementations of existing methods to ensure homogeneous evaluation of performance, and we show that our implementations perform as well or better than existing available implementations. Finally, we propose simplified variants of standard approaches and show that they are faster than their fully-fledged counterparts in 59 of 62 experiments.
Provider's Constraints and Difficulties in Primary Health Care System

Background: The contractualization of human resource in recent years has resulted into various human resource management issues. Objective: To explore the administrative and management issues of contractual model of human resource under primary health care system in Delhi. Materials and Methods: Comparative study was conducted on randomly selected sample of 333, comprised of Medical Officers, ANMs, Pharmacist and Laboratory Assistants and Technicians, both regular and contractual cadre. The data was collected using the semi-structured interview schedule and thematic content analysis was done. Results: The five major themes emerged in the analysis; these are (i) physical infrastructure, (ii) organization's working environment, (iii) privileges of staff, (iv) discontentment, (v) human resource development. Comparative analysis of themes between regular and contractual staff revealed significant differences in factors which are embedded into the organization's culture. Element of discontentment is high amongst contractual staff particularly for discrimination in job, undermining of authority, patient care relationship and privileges provided to regular staff. This reflects the area of dissatisfaction which varies between regular and contractual staff in the organization. Conclusion: If primary health care system fails to address genuine constraints of human resources of both regular and contractual cadre and perception of discrimination persists, it is bound to result into poor motivation for good performance in the system of health care. So, adopting good practices in human resource management keeping regular and contractual employees grievances at forefront are urgently needed to ensure the availability of adequately trained and motivated personnel's in health facilities.
Using counterfactual regret minimization to create competitive multiplayer poker agents

Games are used to evaluate and advance Multiagent and Artificial Intelligence techniques. Most of these games are deterministic with perfect information (e.g. Chess and Checkers). A deterministic game has no chance element and in a perfect information game, all information is visible to all players. However, many real-world scenarios with competing agents are stochastic (non-deterministic) with imperfect information. For two-player zero-sum perfect recall games, a recent technique called Counterfactual Regret Minimization (CFR) computes strategies that are provably convergent to an e-Nash equilibrium. A Nash equilibrium strategy is useful in two-player games since it maximizes its utility against a worst-case opponent. However, for multiplayer (three or more player) games, we lose all theoretical guarantees for CFR. However, we believe that CFR-generated agents may perform well in multiplayer games. To test this hypothesis, we used this technique to create several 3-player limit Texas Hold'em poker agents and two of them placed first and second in the 3-player event of the 2009 AAAI/IJCAI Computer Poker Competition. We also demonstrate that good strategies can be obtained by grafting sets of two-player subgame strategies to a 3-player base strategy after one of the players is eliminated.
Comorbidities Associated with Urinary Incontinence: A Case-Control Study from the Second Dutch National Survey of General Practice

Purpose: The aim of this study was to identify which comorbidities are more common in patients with urinary incontinence compared with patients without this diagnosis. Design of study: Case-control study. Setting/methods: The data for this study were obtained from the Second Dutch National Survey of General Practice (DNSGP-2) performed in 2001 and were extracted from the electronic medical records of all patients registered in the participating practices in the year of study (2001). Conditional logistic regression was performed using the PHREG (proportional hazards regression) procedure. Results: Urinary tract infections, constipation, and depression were more prevalent in both men and women with urinary incontinence than in controls. In men, heart failure is more common than among controls, and in women, diabetes mellitus, genitourinary prolapse, and chronic obstructive pulmonary disease (COPD)/asthma are more common than among controls. Conclusion: General practitioners could ask for the presence of urinary incontinence in patients with the above described comorbidities.
A Constraint-based and Head-driven Analysis of Multiple Nominative Constructions∗

(1) a. K: John-i emeni-ka chincelha-si-ta. John-NOM mother-NOM kind-NOM-DECL ‘It is John whose mother is kind. ’ ∗An earlier version of this paper was presented at HPSG-2000: The 7th International Conference on HPSG at UC Berkeley, California, 22-23 July 2000. I have been benefited from suggestions and criticisms from Chan Chung, Byung-Soo Park, Ivan Sag, Peter Sells, Gert Webelhuth, Shuiche Yatabe, and the audiences in the conference. All errors of course remain mine. There are several other types of double nominative constructions that we do not discuss in this paper:
APPLYING HYBRID GENETIC ALGORITHMS TO RECOVER FOCAL LENGTH , CAMERA MOTION AND 3 D MODELS FROM SILHOUETTES

In this paper, a hybrid method is applied to recove r parameters and motion of camera from a set of silhouettes of an object taken under circular motio n. Camera parameters can be obtained by maximizing the total coherence between all silhouettes. Two optimi zation methods, the Powell optimizer (PO) and the Genetic algorithms (GA), are applied to maximize th silhouette coherence and their performances are compared for several experiments. To take advantage of the strengths of the two methods, we developed a hybrid method that combines the genetic algorithm a nd the Powell optimizer to improve the performances in term of convergence speed and accuracy. The reco vered parameters are used for 3D image-based modeling to obtain high fidelity 3D reconstruction.
Evidence for coexistence of enkephalin and glutamate in axon terminals and cellular sites for functional interactions of their receptors in the rat locus coeruleus

The authors previously showed that a subset of axon terminals in the locus coeruleus (LC) contains methionine5‐enkephalin (ENK) and γ‐aminobutyric acid (GABA) immunoreactivities. However, numerous ENK‐labeled terminals lacked GABA and exhibited synaptic specializations that were characteristic of excitatory‐type transmitters. To determine whether ENK coexists with glutamate in the LC, preembedding immunoperoxidase detection of ENK or immunogold‐silver was combined with postembedding identification of glutamate using a gold marker. Indeed, 28% of the ENK‐labeled axon terminals examined (n = 250 axon terminals) also contained glutamate. To define further sites for functional interactions between opiate ligands and excitatory amino acid receptors, the ultrastructural localization of the μ‐opioid receptor (MOR) was examined with respect to either the kainate receptor (KAR) or the R1 subunit of the N‐methyl‐D‐aspartate (NR1)‐type glutamate receptor in the LC. Gold‐silver labeling for MOR and peroxidase labeling for either KAR or NR1 indicated that the MOR often was localized to the plasma membrane of dendrites that also exhibited immunolabeling for either glutamate receptor subtype. In contrast to the KAR, which was identified primarily in somata and dendrites, NR1 immunoreactivity also was found frequently in axon terminals as well as in glial processes. Glial processes containing NR1 occasionally exhibited immunolabeling for MOR and sometimes were directly apposed to MOR‐containing dendrites in the LC. Furthermore, NR1‐labeled receptors in axon terminals sometimes were presynaptic to MOR‐labeled dendrites. The authors concluded that ENK and glutamate may be cotransmitters in LC afferents. Moreover, ligands at the KAR may modulate directly MOR‐containing neurons in the LC, whereas actions at NR1 receptors may affect opioid‐sensitive neurons through multiple cellular mechanisms, i.e., through presynaptic, postsynaptic, or glial actions. J. Comp. Neurol. 417:103–114, 2000. ©2000 Wiley‐Liss, Inc.
Floating-Point Fused Multiply-Add Architectures

Two new floating-point fused multiply-add architectures for the single instruction execution of (A times B) + C are presented. The three-path architecture uses parallel hardware paths similar to those in dual-path floating-point adders. The new bridge architecture re-uses common floating-point components to add a fused multiply-add instruction. Each new architecture as well as a collection of floating-point arithmetic units and a classic fused multiplier-adder have been designed using the advanced micro devices 65 nanometer silicon on insulator CMOS technology to fairly compare the new architectures.
Differential roles of regulatory light chain and myosin binding protein‐C phosphorylations in the modulation of cardiac force development

Phosphorylation of myosin regulatory light chain (RLC) by myosin light chain kinase (MLCK) and myosin binding protein‐C (cMyBP‐C) by protein kinase A (PKA) independently accelerate the kinetics of force development in ventricular myocardium. However, while MLCK treatment has been shown to increase the Ca2+ sensitivity of force (pCa50), PKA treatment has been shown to decrease pCa50, presumably due to cardiac troponin I phosphorylation. Further, MLCK treatment increases Ca2+‐independent force and maximum Ca2+‐activated force, whereas PKA treatment has no effect on either force. To investigate the structural basis underlying the kinase‐specific differential effects on steady‐state force, we used synchrotron low‐angle X‐ray diffraction to compare equatorial intensity ratios (I1,1/I1,0) to assess the proximity of myosin cross‐bridge mass relative to actin and to compare lattice spacings (d1,0) to assess the inter‐thick filament spacing in skinned myocardium following treatment with either MLCK or PKA. As we showed previously, PKA phosphorylation of cMyBP‐C increases I1,1/I1,0 and, as hypothesized, treatment with MLCK also increased I1,1/I1,0, which can explain the accelerated rates of force development during activation. Importantly, interfilament spacing was reduced by ∼2 nm (Δ 3.5%) with MLCK treatment, but did not change with PKA treatment. Thus, RLC or cMyBP‐C phosphorylation increases the proximity of cross‐bridges to actin, but only RLC phosphorylation affects lattice spacing, which suggests that RLC and cMyBP‐C modulate the kinetics of force development by similar structural mechanisms; however, the effect of RLC phosphorylation to increase the Ca2+ sensitivity of force is mediated by a distinct mechanism, most probably involving changes in interfilament spacing.
Effects of the Gold Nanoparticles (AuNPs) on the Proliferation and Morphological Characteristics of Human Breast Cancer Cells (MCF-7) in Culture

Ultrastructural characteristic and morphological changes of untreated and treated breast cancer MCF-7 cells were observed by energy-filtered transmission electron microscope (EFTEM). Morphological observation of MCF-7 after being treated with 13 nm, 50 nm, and 70 nm AuNPs, were looking unhealthy and dying out of the populace, the observed cells were more reduced and dying as treatment with 50 nm and 70 nm AuNPs. Cells detachment, clumping, shrunken, and dispersed cells in the culture medium and floating cells were also observed. The observed morphological changes increase in 50 nm and 70 nm AuNPs than in 13 nm AuNPs, which is less toxic to MCF-7 cells. The presented morphological analysis has established that 13 nm AuNPs showed less toxic to MCF-7 breast cancer cells. Whereas, control cells of MCF-7 were treated with only complete culture media, despite the duration of treatment, whereby the cells maintained most of their morphological features and observed to have a typical morphology of healthy cells that are well attached to the surface. These results indicate that AuNPs were clustered in the cells and there was no significant difference between images of different sizes of AuNPs observed in the cells, because the AuNPs always clustered together inside the cells.
Chest physical therapy for children hospitalised with acute pneumonia: a randomised controlled trial

Background: The indication for chest physical therapy as an adjunct to the treatment of children hospitalised with acute pneumonia remains controversial and there is a lack of robust scientific evidence for the effectiveness of this modality in these patients. Methods: A randomised controlled trial was conducted in two tertiary hospitals in southern Brazil. Children aged 29 days to 12 years hospitalised with pneumonia between February and October 2006 were recruited; 51 were randomly allocated to the intervention group (chest physical therapy plus standard treatment for pneumonia) and 47 to the control group (standard treatment for pneumonia alone). The primary outcome was time to clinical resolution. The secondary outcomes were length of stay in hospital and duration of respiratory symptoms and signs. Results: There were no significant differences in terms of median time to clinical resolution (4.0 vs 4.0 days, p = 0.84) and median length of hospital stay (6.0 vs 6.0 days, p = 0.76) between the intervention and control groups. The intervention group had a longer median duration of coughing (5.0 vs 4.0 days, p = 0.04) and of rhonchi on lung auscultation (2.0 vs 0.5 days, p = 0.03) than the control group. Conclusions: Chest physical therapy as an adjunct to standard treatment does not hasten clinical resolution of children hospitalised with acute pneumonia and may prolong duration of coughing and rhonchi.