Miracle-dz/UniFAR-FTUs huggingface dataset:
Crystal structure of oxidized trimethylamine N-oxide reductase from Shewanella massilia at 2.5 A resolution.

The periplasmic trimethylamine N-oxide (TMAO) reductase from the marine bacteria Shewanella massilia is involved in a respiratory chain, having trimethylamine N-oxide as terminal electron acceptor. This molybdoenzyme belongs to the dimethyl sulfoxide (DMSO) reductase family, but has a different substrate specificity than its homologous enzyme. While the DMSO reductases reduce a broad spectra of organic S-oxide and N-oxide compounds, TMAO reductase from Shewanella massilia reduces only TMAO as the natural compound. The crystal structure was solved by molecular replacement with the coordinates of the DMSO reductase from Rhodobacter sphaeroides. The overall fold of the protein structure is essentially the same as the DMSO reductase structures, organized into four domains. The molybdenum coordination sphere is closest to that described in the DMSO reductase of Rhodobacter capsulatus. The structural differences found in the protein environment of the active site could be related to the differences in substrate specificity of these enzymes. In close vicinity of the molybdenum ion a tyrosine residue is missing in the TMAO reductase, leaving a greater space accessible to the solvent. This tyrosine residue has contacts to the oxo groups in the DMSO reductase structures. The arrangement and number of charged residues lining the inner surface of the funnel-like entrance to the active site, is different in the TMAO reductase than in the DMSO reductases from Rhodobacter species. Furthermore a surface loop at the top of the active-site funnel, for which no density was present in the DMSO reductase structures, is well defined in the oxidized form of the TMAO reductase structure, and is located on the border of the funnel-like entrance of the active center.
Multiscale Segmentation of Unstructured Document Pages Using Soft Decision Integration

We present an algorithm for layout-independent document page segmentation based on document texture using multiscale feature vectors and fuzzy local decision information. Multiscale feature vectors are classified locally using a neural network to allow soft/fuzzy multi-class membership assignments. Segmentation is performed by integrating soft local decision vectors to reduce their "ambiguities".
Discovering Available Drinks Through Natural , Robot-Led , Human-Robot Interaction Between a Waiter and a Bartender

This research focuses on natural, robot-led, human-robot interaction that enables a robot to discover what drinks a bartender can prepare through continuous application of speech recognition, understanding and generation. Speech was recognised using Google Cloud's speech to text API, understood by matching either the object or main verb of a sentence against a list of key words and, finally, generated using templates with variable parts. The difficulty lies in the large quantity of key words, as they are based on the properties of the ordered drinks. The results show that having the aforementioned interaction works well to some extent, i.e. the naturalness of the interaction was ranked 5.5 on average. Furthermore, the obtained precision when identifying the unavailable drinks was 0.625 and the obtained recall was 1, resulting in an F1 measure of 0.769.
The relationship between serum anti-Müllerian hormone levels and the follicular arrest for women with polycystic ovary syndrome

Abstract The aim of this study was to ascertain whether higher levels of serum anti-Müllerian hormone (AMH) are associated with the ovarian follicular arrest in women with polycystic ovary syndrome (PCOS). This prospective study compared AMH levels between serum and dominant follicular fluid (FF) in ovulatory polycystic ovary (PCO) women and anovulatory (menstrual cycle ≥60 days.) PCOS women. All 102 women provided a baseline hormone profile and underwent controlled ovarian hyperstimulation (COH). The anovulatory PCO women had a similar body mass index (BMI), antral follicle count (AFC), and baseline serum AMH levels as the ovulatory PCO women except that their median luteinizing hormone (LH; 10.0 mIU/ml), testosterone (T) (0.61 ng/l), and androstenedione (A) (3.47 ng/l) levels were significantly higher than ovulatory PCO women (4.9 mIU/m; 0.43 ng/l and 2.09 ng/l, respectively). The ovarian response to gonadotropin stimulation during COH including serum AMH on the day of HCG administration and dominant FF AMH at 36 hours after HCG administration, total follicle stimulating hormone (FSH) dose administrated, peak E2, (estrogen) levels and number of occytes retrieved were all similar between women with anovulatory and ovulatory PCO. Using multiple regression analysis it was found that an important independent determinant affecting AMH was AFC, as opposed to LH and T. Logistic regression analysis showed that the two most important factors affecting ovulation were serum LH and T, whereas serum AMH and AFC were not selected for inclusion in the model. The reduction in AMH during COH occurs as a consequence of dominant follicles with a corresponding reduction in small antral follicle number. Elevated serum AMH levels in PCO women seem to be related only to follicular excess and not follicular arrest.
ROLE DE L'AVERSION GUSTATIVE CONDITIONNEE ET DE LA SATIETE DANS LA DEPRESSION DE LA PRISE ENERGETIQUE INDUITE PAR LES REGIMES HYPERPROTEIQUES CHEZ LE RAT

LES REGIMES HYPERPROTEIQUES INDUISENT UNE DEPRESSION DE LA PRISE ENERGETIQUE CHEZ LE RAT. LES MECANISMES SOUS-TENDANT CETTE DEPRESSION SONT MAL CONNUS. L'OBJET DE CETTE THESE EST D'ANALYSER LES ROLES RESPECTIFS DE LA PALATABILITE, DE LA SATIETE, ET DE L'AVERSION GUSTATIVE CONDITIONNEE DANS CE PHENOMENE. LAPPLICATION DE LA METHODE DENREGISTREMENT DE LA PRISE ALIMENTAIRE ET DE VIDEO ANALYSE A DES RATS, LORS DE LA TRANSITION DUN REGIME NORMOPROTEIQUE (14%) VERS UN REGIME HYPERPROTEIQUE (>50%), MONTRE DES MODIFICATIONS TRANSITOIRES DU COMPORTEMENT DE LANIMAL LORS DU PREMIER JOUR : REDUCTION DE LA TAILLE DU REPAS, DIMINUTION DE LA VITESSE DINGESTION ET MODIFICATION DE LA SEQUENCE COMPORTEMENTALE DE SATIETE. APRES ADAPTATION AU REGIME HYPERPROTEIQUE, LA QUANTITE DENERGIE INGEREE AVEC LE REGIME HYPERPROTEIQUE RESTE NEANMOINS EN DECA DE CELLE INGEREE EN REGIME NORMOPROTEIQUE ET LE POIDS DES ANIMAUX RECEVANT UN REGIME HYPERPROTEIQUE EST PLUS FAIBLE. DES LE SECOND OU TROISIEME JOUR, SELON LA PROTEINE ALIMENTAIRE UTILISEE, LA SEQUENCE COMPORTEMENTALE DE SATIETE N'EST PLUS DIFFERENTE DE CELLE INDUITE PAR UN REPAS NORMOPROTEIQUE. L'ABSENCE D'AVERSION GUSTATIVE CONDITIONNEE ET LA PRESENCE D'UN EFFET SATIETOGENE DES PROTEINES A ETE CONFIRMEE QUAND LES RATS, ELEVES SUR UN REGIME NORMOPROTEIQUE, ET RECEVANT TROIS REPAS PAR JOUR, INGERENT UN EN-CAS PROTEINE. LES PROTEINES DEPRIMENT PLUS LA PRISE ALIMENTAIRE LORS DU REPAS SUIVANT QUE LES GLUCIDES. LANALYSE DE LA SEQUENCE ALIMENTAIRE MONTRE QUE LA DIMINUTION DE LA TAILLE DU REPAS INDUITE PAR LES CHARGES PROTEIQUES 35% ET 50% EST DU A UN EFFET SATIETOGENE ET NON A UNE AVERSION GUSTATIVE CONDITIONNEE. NOTRE ETUDE A AUSSI MONTRE QUE PLUSIEURS PARAMETRES BIOCHIMIQUES (AMINOACIDEMIE TOTALE, ACIDES AMINES BRANCHES ) OU HORMONAUX (LEPTINEMIE) SONT SUSCEPTIBLES DETRE A LA BASE DES SIGNAUX ENVOYES AU CERVEAU POUR INITIER LA BAISSE DE PRISE ALIMENTAIRE. EN RESUME, LES RATS NE DEVELOPPENT PAS UNE AVERSION GUSTATIVE CONDITIONNEE VIS A VIS DU REGIME HYPERPROTEIQUE. LES MODIFICATIONS DE LA PRISE ALIMENTAIRE ET DU COMPORTEMENT, CORRESPONDENT PLUS A UN EFFET SUR-SATIETOGENE DU REGIME HYPERPROTEIQUE COMBINE A SA FAIBLE PALATABILITE ET A UNE NECESSAIRE ADAPTATION METABOLIQUE DE L'ANIMAL A CE REGIME. NOS RESULTATS, QUE CE SOIT DANS LE CADRE DE L'INGESTION D'UN REGIME HYPERPROTEIQUE OU, PLUS SIMPLEMENT LORS D'UN REPAS, MONTRE QUE L'INGESTION DE PROTEINES S'ACCOMPAGNE D'UN EFFET SATIETOGENE QUI RESTE A EXPLIQUER
Transcriptomic Diversification of Developing Cumulus and Mural Granulosa Cells in Mouse Ovarian Follicles1

ABSTRACT Cumulus cells and mural granulosa cells (MGCs) have functionally distinct roles in antral follicles, and comparison of their transcriptomes at a global and systems level can propel future studies on mechanisms underlying their functional diversity. These cells were isolated from small and large antral follicles before and after stimulation of immature mice with gonadotropins, respectively. Both cell types underwent dramatic transcriptomic changes, and differences between them increased with follicular growth. Although cumulus cells of both stages of follicular development are competent to undergo expansion in vitro, they were otherwise remarkably dissimilar with transcriptomic changes quantitatively equivalent to those of MGCs. Gene ontology analysis revealed that cumulus cells of small follicles were enriched in transcripts generally associated with catalytic components of metabolic processes, while those from large follicles were involved in regulation of metabolism, cell differentiation, and adhesion. Contrast of cumulus cells versus MGCs revealed that cumulus cells were enriched in transcripts associated with metabolism and cell proliferation while MGCs were enriched for transcripts involved in cell signaling and differentiation. In vitro and in vivo models were used to test the hypothesis that higher levels of transcripts in cumulus cells versus MGCs is the result of stimulation by oocyte-derived paracrine factors (ODPFs). Surprisingly ∼48% of transcripts higher in cumulus cells than MGCs were not stimulated by ODPFs. Those stimulated by ODPFs were mainly associated with cell division, mRNA processing, or the catalytic pathways of metabolism, while those not stimulated by ODPFs were associated with regulatory processes such as signaling, transcription, phosphorylation, or the regulation of metabolism.
A geometric construction determines all permissible strand arrangements of sandwich proteins.

For a large class of proteins called sandwich-like proteins (SPs), the secondary structures consist of two beta-sheets packed face-to-face, with each beta-sheet consisting typically of three to five beta-strands. An important step in the prediction of the three-dimensional structure of a SP is the prediction of its supersecondary structure, namely the prediction of the arrangement of the beta-strands in the two beta-sheets. Recently, significant progress in this direction was made, where it was shown that 91% of observed SPs form what we here call "canonical motifs. " Here, we show that all canonical motifs can be constructed in a simple manner that is based on thermodynamic considerations and uses certain geometric structures. The number of these structures is much smaller than the number of possible strand arrangements. For instance, whereas for SPs consisting of six strands there exist a priori 900 possible strand arrangements, there exist only five geometric structures. Furthermore, the few motifs that are noncanonial can be constructed from canonical motifs by a simple procedure.
University of Groningen Normal-Hearing Listeners’ and Cochlear Implant Users’ Perception of Pitch Cues in Emotional Speech Gilbers,

In cochlear implants (CIs), acoustic speech cues, especially for pitch, are delivered in a degraded form. This study’s aim is to assess whether due to degraded pitch cues, normal-hearing listeners and CI users employ different perceptual strategies to recognize vocal emotions, and, if so, how these differ. Voice actors were recorded pronouncing a nonce word in four different emotions: anger, sadness, joy, and relief. These recordings’ pitch cues were phonetically analyzed. The recordings were used to test 20 normal-hearing listeners’ and 20 CI users’ emotion recognition. In congruence with previous studies, high-arousal emotions had a higher mean pitch, wider pitch range, and more dominant pitches than low-arousal emotions. Regarding Corresponding author: Steven Gilbers, Center for Language and Cognition Groningen, Department of Applied Linguistics, University of Groningen, Oude Kijk in ‘t Jatstraat 26, 9712 EK Groningen, The Netherlands. Email: s.r. k.i. gilbers@rug.nl i-Perception
Genetic control of development in Volvox: isolation and characterization of morphogenetic mutants.

Morphogenetic mutants of the colonial green alga, Volvox carteri f. nagariensis, were induced by chemical mutagenesis. The 68 independent mutants are classified into 12 readily identifiable phenotypes affecting various stages of asexual development. Nine of the mutants are temperature sensitive with normal development at 25 degrees and mutant development occurring at 35 degrees . Some mutant genes appear to be involved in the regulation of differentiation or the stability of the differentiated state. Other mutations occur in genes apparently responsible for structural components of dividing cells or adult colonies. Two mutants affect different aspects of the posterior-anterior polarization of the mature colony. One mutation affects a gene which acts very early in colonial development, but affects the appearance of the mature colony. The mutants isolated demonstrate the feasibility of using Volvox to study the genetic control of early steps in embryogenesis.
Cerebral white matter hyperintensities (WMH): an analysis of cerebrovascular risk factors in Lebanon

Background: Cerebral white matter hyperdensities (WMH) are frequently reported on brain magnetic resonance images (MRI) of elderly people; its significance is still under debate. Methods: WMH subtypes may correlate with vascular risk factors, such as aging, hypertension (HTN) and diabetes mellitus (DM). The suggested hypothesis was to find if any of the periventricular WMH (PVWMH) or the deep WMH (DWMH) would be significantly more correlated with the above vascular risk factors. According to the Fazekas semiquantitative rating scale, we classified WMH into four subtypes: (1) absence of WMH, (2) presence of DWML, (3) presence of PVWMH, (4) presence of both DWML and PVWML. The study was performed on 257 Lebanese inpatients aged 40 years and above who underwent a brain MRI, regardless of their underlying pathology and who were admitted to an Internal Medicine Department in Beirut. The study patients were categorized into five subgroups by age intervals of 10 years. Results: Mean age was 62; 54.1% were females; WMH were observed in 59.5% of study population; we found a linear correlation with WMH and aging with a clear shift for patients over age 60, reaching 84% in patients subgroup of 70–79-year-old and 94% patients subgroup over 80-year-old. PVWMH was found significantly more frequently and in linear correlation with aging and HTN. WMH were also found more frequently among the DM individuals. Conclusion: From this first ever retrospective Lebanese study, WMH was reported increasingly with aging in accordance with data from the literature; PVWMH was found significantly more correlated with aging and HTN than was DWMH alone.
Therapeutic Relationships and Quality of Life: Association of Two Subjective Constructs in Schizophrenia Patients

Subjective quality of life is an important criterion in outcome evaluation that has been well-researched in psychiatry. By comparison, the therapeutic relationship which may also be subjectively assessed has been relatively neglected as an outcome criterion although it has predictive power in relation to outcome. This exploratory study investigated subjective quality of life and therapeutic relationships in first-admission (N = 90) and long-term (N=168) schizophrenia patients, each at two points of time. The follow-up period was 9 months for the first-admission sample and 1.5 years for the long-term sample. A significant relationship was found between global assessments of quality of life and therapeutic relationships in long-term, but not in first-admission patients. This finding was consistent at both assessments, suggesting that therapeutic relationships may become more central to quality of life in long-term care situations and that patients' views of this relationship are increasingly embedded in their overall appraisal of life.
Absorptive Frequency-Selective Reflection and Transmission Structures

Tailoring methodology is proposed in this communication to achieve an arbitrary frequency response within a wide absorption band. An ultrawideband (UWB) absorber utilizing multiple resonances in the unit cell of 3-D frequency-selective structure is utilized as the textile for the proposed designs. Two types are proposed: one is absorptive frequency-selective reflection structure (AFSR) and the other is absorptive frequency-selective transmission structure (AFST). These structures have reflection/transmission band within a wide absorption band. Two prototypes are designed, fabricated, and measured to validate the proposed methodology. The first one is an UWB absorber with 155.7% absorption bandwidth from 1.8 to 14.4 GHz with structure’s thickness of $0.12\lambda _{0}$ at the lowest absorption frequency. The second one is an AFST with wide absorption bands at both sides of its transmission window. It exhibits 54% and 76% for the lower and upper absorption bands, respectively, with 1 dB insertion loss in the transmission window. A good agreement is achieved between simulation and measured results.
Hypouricemia and tubular transport of uric acid

La hipouricemia se diagnostica cuando los niveles plasmáticos de ácido úrico son menores o iguales a 2,0 mg/dl. El diagnóstico diferencial de la hipouricemia se realiza en función de la excreción fraccional de ácido úrico, y se han identificado varios transportadores y proteínas implicados en el manejo del ión urato en el túbulo proximal. En este artículo se revisan los conocimientos actuales sobre el manejo tubular renal del ácido úrico y las distintas situaciones clínicas asociadas con hipouricemia.
Carcinoma mucinoso de la mama: características clínicas, biológicas y pronósticas en comparación con las del ductal infiltrante de tipo clásico

SUMMARY To investigate the existence of possible clinical differences between the pure mucinous breast carcinoma (MC) and the classic inﬁltrant ductal breast carcinoma of classic type (DCC). It is a retrospective study comparing two different populations of 60patients with MC and another one of 232patients with DCC.Clinic-pathologic characteristics of the tumours and prognosis from patients were compared. There are signiﬁcant differences between these two groups of patients with regard to age from patients,size and nodal status from tumours,and prognosis from patients.Thus,patients with MC were signiﬁcantly (p < 0.05) older (mean 6 SE:67.9 6 1.6years) than patients with DCC (mean 6 SE: 58.6 6 0.9years). Furthermore,the patients with MC showed a percentage of tumours of small size (T1:36.7% and T2:55%) signiﬁcantly (p < 0.001) higher than patients with DCC (T1:27.1% and T2:46.9%). Likewise,the percentage of node-positive cases was signiﬁcantly (p < 0.05) lower in MC than in DCC (15.0% vs 50.9%). Finally,patients with MC had longer relapse-free survival and overall survival periods than patients with DCC (p < 0.001). These results suggest that MC of the breast have a less aggressive biological behaviour than DCC. Palabras
Comparative Study of Genetic Variation at 15 STR Loci in Three Isolated Populations of the Bosnian Mountain Area

Fifteen autosomal STR loci (D3S1358, TH01, D21S11, D18S51, Penta E, D5S818, D13S317, D7S820, D16S539, CSF1PO, Penta D, VWA, D8S1179, TPOX, and FGA) were studied in three geographically close but isolated populations from the Bosnian mountain area. The three villages are Bobovica, Dejcici, and Lukomir. DNA was obtained from 83 individuals, and the allele frequencies and genetic diversity among the three sample groups were compared. In addition, seven of the STR loci (CSF1PO, D13S317, D3S1358, D5S818, D7S820, FGA, TH01) were used in a comparative population analysis of the Bjelas;aknica-Treskavica region and the Adriatic islands of Brac, Hvar, and Korcula. Although the sample sizes are relatively small, the observed variation within any of the small isolated populations is high and comparable to less isolated groups. In addition, even though the populations are geographically isolated, the STR data are similar among the populations. The most significant frequency differences were observed at the TH01 locus. Although the specific allele distributions in any untyped population cannot be determined a priori, we find support for a high degree of diversity for the STR loci in most populations. In addition, the multiple locus profile is highly informative not only for various population studies but also for forensic studies, even when specific population data are not available.
Functional Analysis of RNA Binding by the Hepatitis C Virus RNA-dependent RNA Polymerase*

Protein-RNA interaction plays a critical role in regulating RNA synthesis by the hepatitis C virus (HCV) RNA-dependent RNA polymerase (RdRp). RNAs of 7 nucleotides (nt) or longer had affinities 5-fold better than an RNA of 5 nt, suggesting a minimal length required for binding. To identify RNA contact sites on the HCV RdRp, a biotinylated 7-nt RNA capable of directing de novo initiation was used in a process that coupled reversible formaldehyde cross-linking, RNA affinity chromatography, and mass spectrometry. By this process, we identified 18 peptides cross-linked to the 7-nt RNA. When these identified peptides were overlaid on the three-dimensional structures of NS5B, most mapped to the fingers subdomain, connecting loops between fingers and thumb subdomains and in the putative RNA binding channel. Two of the identified peptides resided in the active site cavity of the RdRp. Recombinant HCV RdRp with single residue changes in likely RNA contact sites were generated and characterized for effects on HCV RdRp activity. Mutant proteins had significant effects on cross-linking to 7-nt RNA and reduced RNA synthesis in vitro by 2- to 20-fold compared with wild type protein. When the mutations were tested for the replication of HCV RNA in the context of the cells transfected with the HCV subgenomic replicon, all except one prevented colony formation, indicating a defect in HCV RNA replication. These biochemical and functional analyses identified a number of residues in the HCV RdRp that are important for HCV RNA synthesis.
A hybrid feature selection for network intrusion detection systems: Central points

Network intrusion detection systems are an active area of research to identify threats that face computer networks. Network packets comprise of high dimensions which require huge effort to be examined effectively. As these dimensions contain some irrelevant features, they cause a high False Alarm Rate (FAR). In this paper, we propose a hybrid method as a feature selection, based on the central points of attribute values and an Association Rule Mining algorithm to decrease the FAR. This algorithm is designed to be implemented in a short processing time, due to its dependency on the central points of feature values with partitioning data records into equal parts. This algorithm is applied on the UNSW-NB15 and the NSLKDD data sets to adopt the highest ranked features. Some existing techniques are used to measure the accuracy and FAR. The experimental results show the proposed model is able to improve the accuracy and decrease the FAR. Furthermore, its processing time is extremely short.
A Brief History of Stigmergy

Stigmergy is a class of mechanisms that mediate animal-animal interactions. Its introduction in 1959 by Pierre-Paul Grass made it possible to explain what had been until then considered paradoxical observations: In an insect society individuals work as if they were alone while their collective activities appear to be coordinated. In this article we describe the history of stigmergy in the context of social insects and discuss the general properties of two distinct stigmergic mechanisms: quantitative stigmergy and qualitative stigmergy.