Miracle-dz/UniFAR-FTUs huggingface dataset:
Increases in Entamoeba histolytica Antibody–Positive Rates in Human Immunodeficiency Virus–Infected and Noninfected Patients in Japan: A 10-Year Hospital-Based Study of 3,514 Patients

Serological evidence of the epidemiological trends in Entamoeba histolytica infection is scarce, especially in nonendemic countries. We aimed to determine the antibody-positive rates over a 10-year period, and compare the trends between human immunodeficiency virus (HIV)–infected and –noninfected patients. We reviewed 3,514 patients who underwent antibody testing during the study periods, which were divided into five annual categories: 2004–2005, 2006–2007, 2008–2009, 2010–2011, and 2012–2013. Anti-E. histolytica antibody was assessed by indirect immunofluorescence assay. The antibody-positive rate increased yearly from 2004–2005 to 2012–2013 (P < 0.001), although there was no increase in the annual number of antibody tests. This trend was seen among males (18.6–28.3%; P < 0.01), females (5.4–28.2%; P < 0.01), HIV-infected patients (18.4–26.9%; P < 0.001), and non-HIV-infected patients (14.6–36.8%; P < 0.001), and HIV-infected men who have sex with men (19.4–29.1%; P < 0.001). Among antibody-positive patients, there was a significant increase in the proportion of patients with high (≥ 1,600) titers (0.7–12.9%; P < 0.001), whereas this trend was not seen in patients with low (100) or intermediate (200–800) titers (P = 0.282 and 0.409, respectively). This large hospital-based study demonstrated that positive anti-E. histolytica antibody rates increased over 10 years, even though the annual number of antibody tests remained constant. Moreover, this trend was identified in non-high-risk patients (females and non-HIV-infected patients) as well as in high-risk patients. The proportion of patients with high antibody titers significantly increased among the antibody-positive patients.
Scientific institutions and effective governance: a case study of Chinese stem cell research

In terms of stem cell research, China appears both as a “powerhouse” armed with state-of-the-art facilities, internationally trained personnel and permissive regulation and as a “bit player,” with its capability for conducting high quality research still in question. The gap between China's assiduous endeavors and the observed outcome is due to a number of factors. Based on interviews with 48 key stakeholders active in Chinese stem cell research, this article examines how the structure of scientific institutions has affected effective governance in China. It is demonstrated that despite China's recent efforts to attract highly competent researchers and to launch new regulatory initiatives, the effects of these attempts have been diminished by an absence of middle-layer positions within research teams and by the uncoordinated administrative structures among regulatory bodies.
Epidemiological investigation on depression among 6～16 years old children and adolescents in Chengdu

Objective:To explore the prevalence and co-morbidity in depression disorder among children and adolescents in Chengdu City.Methods:Using a one-phase design,4585 children and adolescents in grades 1~10 were assessed with the Strength and Difficulty questionnaire(SDQ)and Development and Well-Being Assessment(DAWBA). A structured interview with verbatim reports was reviewed by clinicians so that information from parents,teachers,and children were combined in a manner that emulated the clinical process.Results:(1)The rate of depressive disorder was 1.2%,and that in girls was much higher than that in boys after 12 years old(2.56% vs.1.42%). (2)The rate of depressive disorder increased with age from 0.10%(6~8 years)to 2.59%(≥15 years). (3)The co-morbidity was 40%. The most common comorbidity diagnosis was anxiety disorders(29.1%)and behavior disorders(25.5%). Conclusion:The prevalence of depressive disorder among children and adolescents in Chengdu is 1.2%. Gender and age may be the related factors.The co-morbidity is common in children and adolescents with depression disorder.
Clinical Implications and Hospital Outcome of Immune‐Mediated Myositis in Horses

Background Immune‐mediated myositis (IMM) is a cause of rhabdomyolysis, stiffness, and muscle atrophy predominantly affecting Quarter horses. Limited information is available with regard to outcome, prognostic indicators, and associations with concurrent diseases. Hypothesis/Objectives To report outcomes and associations between outcome and clinical and laboratory parameters, and presence of concurrent illness. Animals Sixty‐eight horses; 52 Quarter horses and related breeds and 16 other breeds. Methods Retrospective cohort study (1991–2014). Medical records of horses with histological diagnosis of IMM were reviewed. Data recovery included signalment, laboratory variables, therapy, and outcome. Logistic regression was used to quantify the association between potential prognostic factors and survival to discharge. Results Quarter horses were younger (mean < 4 years, range 3 months–21 years) than other breeds (mean < 10 years, range 1–23 years). Pathogens causing concurrent or recent infection included S. equi equi, S. equi zooepidemicus, C. pseudotuberculosis, Anaplasma phagocytophilum, herpes virus‐1, and influenza. The most common clinical signs consisted of rapidly progressive diffuse symmetrical muscle atrophy (80%), stiff gait (74%), and fever (44%). All horses that received medical therapy immediately upon admission survived to discharge (survival proportion = 87%). Leucocytosis was a common finding (60%). Horses with concurrent fever and other illness had a poor prognosis for hospital discharge. Conclusions and Clinical Importance Horses with IMM can have a favorable outcome. Horses with concurrent fever and another illness had decreased probability of survival to discharge.
The effects of provocation by foods with raised IgG antibodies and additives on the course of Crohn's disease: a pilot study.

BACKGROUND/AIMS This study was designed to assess the role of foods with raised IgG antibodies and additives on the symptoms and inflammation of Crohn's disease. METHODS Eight patients with Crohn's disease in remission were studied. They followed a strict diet during phase I. Then, provocations with two, three-day periods (phases II and III) followed: in phase II, pure forms of foods with high IgG antibodies and in phase III, off-the-shelf forms of those foods were added. Stool samples were collected for fecal calprotectin assay. Blood samples were taken on the 11th and 17th days for highly sensitive C-reactive protein, ferritin, erythrocyte sedimentation rate, white blood cells, and platelets. Patients kept a diet-symptom diary. RESULTS Increased Crohn's disease activity index scores were found statistically significant (p=0.012) between pre- and during the provocation weeks. There were significant increases according to Harvey-Bradshaw Index when the highest values during the phases I, II (p=0.027) and I, III (p=0.027) were compared. The increases in highly sensitive C-reactive protein (p=0.025) and white blood cells (p= 0.036) were found statistically significant. Fecal calprotectin levels showed day-to-day variability. When compared, the levels of fecal calprotectin increased in all patients on the last day of the restriction (10th day) and the first day of the provocation (11th day) with the exception of one patient. CONCLUSIONS Foods with raised IgG antibody levels and food additives can provoke the symptoms and may stimulate the inflammation in patients with Crohn's disease. Addition of a proper diet with restriction of those foods may be beneficial in the medical treatment.
FILM MUSIC AND HEINZ WERNER'S THEORY O F PHYSIOGNOMIC PERCEPTION

Physiognomic perception, a term coined by Heinz Werner, refers to a mode of perception attuned to expression or expressive attributes. The term applies readily to the perception of faces, gestures, intonation, and mood. It has also been implicated in the perception of the arts and music and is therefore relevant to understanding the perception of film that is accompanied by music. The concept of physiognomic perception distinguishes perceptual experience from emotional response. It is proposed that this distinction must be maintained in analyzing the film-music experience and its dynamics in order that perceptual properties of music and film be identified as such instead of spuriously attributed to emotional responses on the part of the film spectator. Furthermore, the concept of physiognomic perception provides an alternative to the view that music contributes to film perception by simply adding associations. In making this argument, the paper reviews the theory of physiognomic perception, citing historical antecedents in classical Greek philosophy relative to physiognomy and physiognomies, and ideas subsequently derived from that intellectual tradition in terms of the musical modes and affections in music, as formulated in medieval and baroque music theory, respectively. Connections are also made with the general notion of "aesthetic perception," Lipps' theory of "empathy," and more contemporary psychological aesthetic ideas of Arnheim and Gibson.
The evolution of the meatal chamber in crocodyliforms

The unique outer ear of crocodylians consists of a large meatal chamber (MC) concealed by a pair of muscular earlids that shape a large part of the animal's head. This chamber is limited medially by the enlarged tympanic membrane. Yet, the anatomy of this distinctive and complex region is underexplored and its evolutionary history untraced. The osteology and soft tissues of the MC in extant crocodylians was analysed to describe it and establish osteological correlates within this region. A broad survey of the osteological correlates was conducted in major clades of fossil crocodyliforms to estimate evolutionary trends of the MC. The reorganization of the MC at the origin of crocodyliforms includes characters also present in more basal taxa such as ‘sphenosuchians’ as well as unique traits of crocodyliforms. Three major patterns are recognized in the MC of basal mesoeucrocodylians. The distinct ‘thalattosuchian pattern’ indicates that extensive modifications occurred in this clade of aquatic fossil crocodyliforms, even when multiple alternative phylogenetic positions are taken into account. Some traits already established in putative closely related clades are absent or modified in this group. The ‘basal notosuchian/sebecian pattern’ is widespread among basal metasuchians, and establishes for the first time characters maintained later in neosuchians and extant forms. The ‘advanced notosuchian pattern’ includes modifications of the MC possibly related to a terrestrial lifestyle and potentially a structure analogous to the mammalian pinna. The main variation in the MC of neosuchians is associated with the homoplastic secondary opening of the cranioquadrate passage. The inferred phylogenetic trends in the crocodyliform MC suggest the great anatomical disparity in this region followed a complex evolutionary pattern, and tympanic hearing played an important role in the origin and diversification of Crocodyliformes.
SOS-based blind channel estimation under space-time block coded transmissions

In this paper, a new blind channel estimation technique for multiple- input multiple-output (MIMO) space-time block coded (STBC) systems is proposed. The technique is solely based on second-order statistics (SOS), and it consists on the extraction of the main eigenvector of a modified correlation matrix. Furthermore, it can be interpreted as a deterministic technique, i.e., in the absence of noise it is able to exactly recover the channel, up to a real scalar, within a finite number of observations. Unfortunately, in many practical cases there exist ambiguities associated to the problem of blind channel estimation from SOS. In order to resolve these problems we propose a new transmission technique, which is based on the combination of different STBCs (code diversity). In the simplest case, this technique reduces to a rotation or permutation of the transmit antennas (non-redundant precoding). Finally, the performance of the proposed method is demonstrated by means of some simulation examples.
O impacto do contexto da disfluência na organização temporal de consoantes na gagueira

Purpose To analyze and compare the voice onset time (VOT) in Brazilian Portuguese speakers who stutter and those who do not, focusing on three different moments of speech: fluent, pre-dysfluent and post-dysfluent environments. Methods Twenty participants (n=10 with stuttering and n=10 without stuttering) were recorded. The data were transcribed and segmented for acoustic analysis, and it was extracted tokens of Brazilian Portuguese voiceless stops /p/, /t/ and /k/. Tokens were classified according to whether they were produced by people who stutter (PWS) or by people who do not stutter (PWnS), and according to their environment in speech (i.e., in fluent speech, pre-dysfluency, and post-dysfluency). For comparisons within groups it were used the Friedman and Wilcoxon tests, and the Mann-Whitney test was used in intergroup comparisons. Statistical analyses were executed using SPSS 14.0 with the significance level set at α=0.05. Results VOT in stuttering and non-stuttering speakers differed most in the environment of pre-dysfluencies, during which stuttering speakers show significantly longer VOT than speakers who do not stutter. After passing through a moment of dysfluency, however, stuttering speakers’ VOT returns to measures similar to non-stuttering speakers’. Conclusion In pre-dysfluent and post-dysfluent speech, PWS produces longer VOT than PWnS. In the fluent speech of PWS, the stops behave differently. The implications of these results for speech motor control are discussed.
Gross Effects on the Nervous System References Cited

Parkinson's Disease (PD) is a degenerative human neuropathology often defined by hypokinesia, resting tremor, muscle rigidity and general muscle weakness (Bowman and Rand, 1980). Two components comprise the overall motor dysfunction: deficit of voluntary activity and invasion of abnormal involuntary motor activity. This first component, hypokinesia or akinesia, is typically manifested by a difficulty or absence of initiating movement. The second component is evidenced by dystonia or tremors occurring during voluntary motion. Resting tremors occur primarily in the hands and ankles at a frequency of 2-6 Hz. Hand tremors involve the involuntary movement of the thumbs and index fingers in a 'pill rolling' type fashion. Additional symptoms include general tetany, deep muscle tremors, arching of the foot, facial rigidity, and slurring of the speech (Marsden, 1990). Dementia, a persistent intellectual impairment, often accompanies advanced PD. Physiological Damage Parkinsonian pathology is contained within the central nervous system and primarily affects dopaminergic neurons in the nigrostriatal tract, located within the basal ganglia of the brain (Stern and Koller, 1993). These neurons, projecting from the ventromedial and ventrolateral tiers of the substantial nigra pars compacta (SNc), are selectively destroyed throughout the course of the disease process. Clinical symptoms of the disease are exhibited upon the 2 loss of approximately 80% of nigral dopaminergic cells (Marsden, 1990). Such neural degeneration results in a severe reduction of striatal (e.g., caudate nucleus, caudate putamen) dopamine. Within the scope of parkinsonian pathology, dopamine is the principally affected neurotransmitter. Concordant with such dopaminergic neuronal loss, levels of dopamine metabolites, dihydroxyphenylacetic acid (DOPAC) and homovanillic acid (HVA) are similarly depressed (Hornykiewiez and Kish, 1987). Studies utilizing immunostaining techniques have discovered significant reductions of the dopamine-specific re-uptake transporter (Niznik et al., 1991) and the reduction or abnormal distribution of tyrosine hydroxylase (TH) (Kastner et al., 1993), a rate-limiting enzyme mediating dopamine synthesis, within postmortem parkinsonian brain samples. Other pathogenic markers, within the scope of idiopathic parkinsonism are compromised mitochondrial respiratory complexes NADH CoQ reductase (Schapira et al., 1992) and α-ketoglutarate dehydrogenase (Mizuno et al., 1994) in postmortem brain tissue. Neural Architecture within the Basal Ganglia Nigrostriatal neurons are components of a superstructure known as the corticostriato-thalamic loop (Fig. 1-1), proposed to be involved in the filtering of sensory information, initiation of motor activity, and protection of the striatum from glutamatergic overstimulation and resultant excitatory cell death (Purves et al., 1997). The primary sensory filter within this system is the thalamus …
Cubic hypersurfaces and integrable systems

Together with the cubic and quartic threefolds, the cubic fivefolds are the only hypersurfaces of odd dimension bigger than one for which the intermediate Jacobian is a nonzero principally polarized abelian variety (p.p.a.v.). In this paper we show that the family of $21$-dimensional intermediate Jacobians of cubic fivefolds containing a given cubic fourfold $X$ is generically an algebraic integrable system. In the proof we apply an integrability criterion, introduced and used by Donagi and Markman to find a similar integrable system over the family of cubic threefolds in $X$. To enter in the conditions of this criterion, we write down explicitly the symplectic structure, known by Beauville and Donagi, on the family $F(X)$ of lines on the general cubic fourfold $X$, and prove that the family of planes on a cubic fivefold containing $X$ is embedded as a Lagrangian surface in $F(X)$. By a symplectic reduction we deduce that our integrable system induces on the nodal boundary another integrable system, interpreted generically as the family of $20$-dimensional intermediate Jacobians of Fano threefolds of genus four contained in $X$. Along the way we prove an Abel-Jacobi type isomorphism for the Fano surface of conics in the general Fano threefold of genus four, and compute the numerical invariants of this surface.
Dissociating the Role of the Orbitofrontal Cortex and the Striatum in the Computation of Goal Values and Prediction Errors

To make sound economic decisions, the brain needs to compute several different value-related signals. These include goal values that measure the predicted reward that results from the outcome generated by each of the actions under consideration, decision values that measure the net value of taking the different actions, and prediction errors that measure deviations from individuals' previous reward expectations. We used functional magnetic resonance imaging and a novel decision-making paradigm to dissociate the neural basis of these three computations. Our results show that they are supported by different neural substrates: goal values are correlated with activity in the medial orbitofrontal cortex, decision values are correlated with activity in the central orbitofrontal cortex, and prediction errors are correlated with activity in the ventral striatum.
Engineering bacteria for production of rhamnolipid as an agent for enhanced oil recovery

Rhamnolipid as a potent natural biosurfactant has a wide range of potential applications, including enhanced oil recovery (EOR), biodegradation, and bioremediation. Rhamnolipid is composed of rhamnose sugar molecule and β‐hydroxyalkanoic acid. The rhamnosyltransferase 1 complex (RhlAB) is the key enzyme responsible for transferring the rhamnose moiety to the β‐hydroxyalkanoic acid moiety to biosynthesize rhamnolipid. Through transposome‐mediated chromosome integration, the RhlAB gene was inserted into the chromosome of the Pseudomonas aeruginosa PAO1‐rhlA− and Escherichia coli BL21 (DE3), neither of which could produce rhamnolipid. After chromosome integration of the RhlAB gene, the constitute strains P. aeruginosa PEER02 and E. coli TnERAB did produce rhamnolipid. The HPLC/MS spectrum showed that the structure of purified rhamnolipid from P. aeruginosa PEER02 was similar to that from other P. aeruginosa strains, but with different percentage for each of the several congeners. The main congener (near 60%) of purified rhamnolipid from E. coli TnERAB was 3‐(3‐hydroxydecanoyloxy) decanoate (C10–C10) with mono‐rhamnose. The surfactant performance of rhamnolipid was evaluated by measurement of interfacial tension (IFT) and oil recovery via sand‐pack flooding tests. As expected, pH and salt concentration of the rhamnolipid solution significantly affected the IFT properties. With just 250 mg/L rhamnolipid (from P. aeruginosa PEER02 with soybean oil as substrate) in citrate–Na2HPO4, pH 5, 2% NaCl, 42% of oil otherwise trapped was recovered from a sand pack. This result suggests rhamnolipid might be considered for EOR applications. Biotechnol. Bioeng. 2007; 98: 842–853. © 2007 Wiley Periodicals, Inc.
Subpopulations of Staphylococcus aureus Clonal Complex 121 Are Associated with Distinct Clinical Entities

We investigated the population structure of Staphylococcus aureus clonal complex CC121 by mutation discovery at 115 genetic housekeeping loci from each of 154 isolates, sampled on five continents between 1953 and 2009. In addition, we pyro-sequenced the genomes from ten representative isolates. The genome-wide SNPs that were ascertained revealed the evolutionary history of CC121, indicating at least six major clades (A to F) within the clonal complex and dating its most recent common ancestor to the pre-antibiotic era. The toxin gene complement of CC121 isolates was correlated with their SNP-based phylogeny. Moreover, we found a highly significant association of clinical phenotypes with phylogenetic affiliations, which is unusual for S. aureus. All isolates evidently sampled from superficial infections (including staphylococcal scalded skin syndrome, bullous impetigo, exfoliative dermatitis, conjunctivitis) clustered in clade F, which included the European epidemic fusidic-acid resistant impetigo clone (EEFIC). In comparison, isolates from deep-seated infections (abscess, furuncle, pyomyositis, necrotizing pneumonia) were disseminated in several clades, but not in clade F. Our results demonstrate that phylogenetic lineages with distinct clinical properties exist within an S. aureus clonal complex, and that SNPs serve as powerful discriminatory markers, able to identify these lineages. All CC121 genomes harboured a 41-kilobase prophage that was dissimilar to S. aureus phages sequenced previously. Community-associated MRSA and MSSA from Cambodia were extremely closely related, suggesting this MRSA arose in the region.
$B$- and $D$-meson decay constants from three-flavor lattice QCD

We calculate the leptonic decay constants ofB (s) andD (s) mesons in lattice QCD using staggered light quarks and Fermilab bottom and charm quarks. We compute the heavy-light meson correlation functions on the MILC asqtad-improved staggered gauge congurations which include the eects of three light dynamical sea quarks. We simulate with several values of the light valence- and sea-quark masses (down to ms=10) and at three lattice spacings (a 0.15, 0.12, and 0.09 fm) and extrapolate to the physical up and down quark masses and the continuum using expressions derived in heavy-light meson staggered chiral perturbation theory. We renormalize the heavy-light axial current using a mostly nonperturbative method such that only a small correction to unity must be computed in lattice perturbation theory and higher-order terms are expected to be small. We obtain f B+ = 196:9(8:9) MeV, fBs = 242:0(9:5) MeV, f D+ = 218:9(11:3) MeV, fDs = 260:1(10:8) MeV, and the SU(3) avor-breaking ratios fBs =fB = 1:229(26) and fDs =fD = 1:188(25), where the numbers in parentheses are the total statistical and systematic uncertainties added in quadrature.