Miracle-dz/UniFAR-FTUs huggingface dataset:
Astrogliosis Associated With Behavioral Abnormality in a Non-anaphylactic Mouse Model of Cow's Milk Allergy

Etiology of neuropsychiatric disorders is complex, involving multiple factors that can affect the type and severity of symptoms. Although precise causes are far from being identified, allergy or other forms of hypersensitivity to dietary ingredients have been implicated in triggering or worsening of behavioral and emotional symptoms, especially in patients suffering from depression, anxiety, attention-deficit hyperactivity, and/or autism. Among such ingredients, cow's milk, along with wheat gluten, is commonly suspected. However, the contributory role of cow's milk in these disorders has not been elucidated due to insufficient pathophysiological evidence. In the present study, we therefore investigated neuroinflammatory changes that are associated with behavioral abnormality using a non-anaphylactic mouse model of cow's milk allergy (CMA). Male and female C57BL/6J mice were subjected to a 5-week oral sensitization procedure without or with a major milk allergen, beta-lactoglobulin (BLG). All mice were then later challenged with BLG, and their anxiety- and depression-associated behaviors were subsequently assessed during the 6th and 7th weeks. We found that BLG-sensitized male mice exhibited significantly increased anxiety- and depression-like behavior, although they did not display anaphylactic reactions when challenged with BLG. Female behavior was not noticeably affected by BLG sensitization. Upon examination of the small intestines, reduced immunoreactivity to occludin was detected in the ileal mucosa of BLG-sensitized mice although the transcriptional expression of this tight-junction protein was not significantly altered when measured by quantitative RT-PCR. On the other hand, the expression of tumor necrosis factor alpha (TNFα) in the ileal mucosa was significantly elevated in BLG-sensitized mice, suggesting the sensitization had resulted in intestinal inflammation. Inflammatory responses were also detected in the brain of BLG-sensitized mice, determined by the hypertrophic morphology of GFAP-immunoreactive astrocytes. These reactive astrocytes were particularly evident near the blood vessels in the midbrain region, resembling the perivascular barrier previously reported by others in experimental autoimmune encephalitis (EAE) mouse models. Interestingly, increased levels of COX-2 and TNFα were also found in this region. Taken together, our results demonstrated that BLG sensitization elicits inflammatory responses in the intestine and brain without overt anaphylactic signs of milk allergy, signifying food allergy as a potential pathogenic factor of neuropsychiatric disorders.
Measurement Variability Following MRI System Upgrade

Major hardware/software changes to MRI platforms, either planned or unplanned, will almost invariably occur in longitudinal studies. Our objective was to assess the resulting variability on relevant imaging measurements in such context, specifically for three Siemens Healthcare Magnetom Trio upgrades to the Prismafit platform. We report data acquired on three healthy volunteers scanned before and after three different platform upgrades. We assessed differences in image signal [contrast-to-noise ratio (CNR)] on T1-weighted images (T1w) and fluid-attenuated inversion recovery images (FLAIR); brain morphometry on T1w image; and small vessel disease (white matter hyperintensities; WMH) on FLAIR image. Prismafit upgrade resulted in higher (30%) and more variable neocortical CNR and larger brain volume and thickness mainly in frontal areas. A significant relationship was observed between neocortical CNR and neocortical volume. For FLAIR images, no significant CNR difference was observed, but WMH volumes were significantly smaller (-68%) after Prismafit upgrade, when compared to results on the Magnetom Trio. Together, these results indicate that Prismafit upgrade significantly influenced image signal, brain morphometry measures and small vessel diseases measures and that these effects need to be taken into account when analyzing results from any longitudinal study undergoing similar changes.
The Fate of Bacteria in Human Digestive Fluids: A New Perspective Into the Pathogenesis of Vibrio parahaemolyticus

Vibrio parahaemolyticus causes the most seafood-attributed gastroenteritis outbreaks worldwide and studies on its pathogenesis during passage through the human digestive fluids are limited. An in vitro continuous model system mimicking passage through saliva, gastric and intestinal fluid was used to study the survival, morphology and virulence-related gene expression of a total of sixty pathogenic, and non-pathogenic V. parahaemolyticus strains. The changes to these three characteristics for the sixty V. parahaemolyticus strains were minimal on passage through the saliva fluid. No V. parahaemolyticus strains survived passage through gastric fluid with low pH values (2.0 and 3.0) and the cells, examined microscopically, were severely damaged. However, when the pH of gastric fluid increased to 4.0, the bacterial survival rate was 54.70 ± 1.11%, and the survival rate of pathogenic strains was higher when compared to non-pathogenic strains. Even though the bactericidal effect of intestinal fluid was lower than gastric fluid, virulence-related gene expression was enhanced in the intestinal fluid. Seafood matrices can significantly raise the pH level of gastric fluid and thus aid the survival of V. parahaemolyticus through passage from human gastric acid and progression of pathogenesis in the intestinal fluid. We confirmed these phenomena in the in vitro continuous digestion model.
Parallels in Processing Boundary Cues in Speech and Action

Speech and action sequences are continuous streams of information that can be segmented into sub-units. In both domains, this segmentation can be facilitated by perceptual cues contained within the information stream. In speech, prosodic cues (e.g., a pause, pre-boundary lengthening, and pitch rise) mark boundaries between words and phrases, while boundaries between actions of an action sequence can be marked by kinematic cues (e.g., a pause, pre-boundary deceleration). The processing of prosodic boundary cues evokes an Event-related Potentials (ERP) component known as the Closure Positive Shift (CPS), and it is possible that the CPS reflects domain-general cognitive processes involved in segmentation, given that the CPS is also evoked by boundaries between subunits of non-speech auditory stimuli. This study further probed the domain-generality of the CPS and its underlying processes by investigating electrophysiological correlates of the processing of boundary cues in sequences of spoken verbs (auditory stimuli; Experiment 1; N = 23 adults) and actions (visual stimuli; Experiment 2; N = 23 adults). The EEG data from both experiments revealed a CPS-like broadly distributed positivity during the 250 ms prior to the onset of the post-boundary word or action, indicating similar electrophysiological correlates of boundary processing across domains, suggesting that the cognitive processes underlying speech and action segmentation might also be shared.
Development and Initial Validation of the Communication About Medication by Providers–Parent Scale (CAMP-P)

This study evaluated the psychometric properties of the Communication about Medication by Providers–Parent Scale (CAMP-P), a 24-item measure of communication relevant to medication adherence between parents and medical providers. Parents of youth (ages 2-7 years) who had received a prescription within the last 12 months completed online surveys regarding demographic and appointment variables, and child’s recent prescription medications, and they completed the newly developed CAMP-P. Exploratory factor analysis of CAMP-P identified 20 items about provider communication corresponding to 3 distinct scales: medication administration strategies, encouraging communication, and addressing barriers to medication taking. Factor scales were related to appointment variables, such as length of time spent discussing medications. The CAMP-P demonstrated good internal consistency and convergent and divergent validity. The CAMP-P is a novel, validated measure of parent perceptions of medication communication and can be utilized to evaluate parent-provider communication on pediatric medication adherence in clinical and research settings.
Postcranial Anatomy of the Rauisuchian Archosaur Batrachotomus kupferzellensis

ABSTRACT Batrachotomus kupferzellensis is an upper Middle Triassic (Late Ladinian) rauisuchian archosaur. The postcranial skeleton of this species is well-represented by fossil material, including the holotype, from the localities of Kupferzell, Crailsheim and Vellberg-Eschenau in southern Germany, and is described here in detail for the first time. All postcranial elements are known except the interclavicle and parts of the carpus, manus, tarsus, pes and some osteoderm and axial elements. B. kupferzellensis is now one of the best-known rauisuchians and will be important in advancing understanding of the group's biology. A period of new anatomical and taxonomic work since 2000 has improved understanding of rauisuchians. Renewed effort in rauisuchian phylogenetics will benefit from these new data, but will also require a careful and detailed approach to character formulation.
Safety and Efficacy of Subcutaneous Pasireotide in Patients With Cushing's Disease: Results From an Open-Label, Multicenter, Single-Arm, Multinational, Expanded-Access Study

Introduction: The efficacy and safety of subcutaneous (sc) pasireotide have been evaluated in a Phase III trial. Here, we report safety and efficacy results from a multinational, expanded-access study of pasireotide sc in patients with Cushing's disease (CD) in a real-world setting (clinicaltrials.gov, identifier: NCT01582061). Methods: Adults with active CD previously untreated with pasireotide were enrolled; pasireotide sc was initiated at 600 μg twice daily (bid; EU countries) or 900 μg bid (non-EU countries; 600 μg bid in patients with impaired glucose metabolism). Pasireotide dose could be adjusted in 300 μg increments/decrements to a maximum of 900 μg bid or minimum of 300 μg bid for sustained urinary free cortisol (UFC) normalization/tolerability issues. Primary objective: document the safety of pasireotide sc in patients with CD. Key secondary objectives: assess the proportion of patients with mean UFC (mUFC) not exceeding the upper limit of normal (ULN) and changes from baseline in clinical signs/symptoms and quality of life (QoL) to weeks 12, 24, and 48. Results: One hundred and four patients received pasireotide: female, n = 84 (80.8%); median duration of pasireotide exposure, 25.1 weeks; median (range) baseline mUFC, 321.2 nmol/24 h (142–10,920; 2.3 × ULN [1.0–79.2]). Forty (38.5%) patients completed the study. The most common reasons for premature discontinuation of pasireotide were unsatisfactory therapeutic effect (n = 26, 25.0%) and adverse events (AEs; n = 20, 19.2%). Drug-related grade 3/4 AEs or drug-related serious AEs (primary endpoint) were documented in 42 (40.4%) patients, most commonly diabetes mellitus (n = 12, 11.5%) and hyperglycemia (n = 8, 7.7%). All patients experienced ≥1 AE and most (n = 102; 98.1%) reported ≥1 drug-related AE; six (5.8%) patients discontinued treatment because of hyperglycemia-related AEs. At weeks 12, 24, and 48, respectively, 36/66 (54.5%), 22/46 (47.8%), and 9/21 (42.9%) evaluable patients had normalized mUFC levels. Clinical signs/symptoms and QoL were also improved. Conclusions: In an international, real-world, clinical-practice setting, pasireotide sc was generally well-tolerated (no new safety signals were identified), effectively reduced UFC (normalization in ~50% of evaluable patients) and improved clinical signs and QoL in patients with CD. While hyperglycemia-related AEs were common, consistent with previous studies, most were manageable, with <6% of patients discontinuing treatment because of these events.
ABC Transporter Genes Show Upregulated Expression in Drug-Resistant Clinical Isolates of Candida auris: A Genome-Wide Characterization of ATP-Binding Cassette (ABC) Transporter Genes

ATP-binding cassette (ABC) superfamily members have a key role as nutrient importers and exporters in bacteria. However, their role as drug exporters in eukaryotes brought this superfamily member to even greater prominence. The capacity of ABC transporters to efflux a broad spectrum of xenobiotics represents one of the major mechanisms of clinical multidrug resistance in pathogenic fungi including Candida species. Candida auris, a newly emerged multidrug-resistant fungal pathogen of humans, has been responsible for multiple outbreaks of drug-resistant infections in hospitals around the globe. Our study has analyzed the entire complement of ABC superfamily transporters to assess whether these play a major role in drug resistance mechanisms of C. auris. Our bioinformatics analyses identified 28 putative ABC proteins encoded in the genome of the C. auris type-strain CBS 10913T; 20 of which contain transmembrane domains (TMDs). Quantitative real-time PCR confirmed the expression of all 20 TMD transporters, underlining their potential in contributing to the C. auris drug-resistant phenotype. Changes in transcript levels after short-term exposure of drugs and in drug-resistant C. auris isolates suggested their importance in the drug resistance phenotype of this pathogen. CAUR_02725 orthologous to CDR1, a major multidrug exporter in other yeasts, showed consistently higher expression in multidrug-resistant strains of C. auris. Homologs of other ABC transporter genes, such as CDR4, CDR6, and SNQ2, also displayed raised expression in a sub-set of clinical isolates. Together, our analysis supports the involvement of these transporters in multidrug resistance in C. auris.
Scale Transfer Modeling: Using Emergent Computation for Coupling an Ordinary Differential Equation System with a Reactive Agent Model

This article deals with the coupling of analytical models with individual based models design with the reactive agents paradigm. Such a coupling of models of different natures is motivated by the need to find a way to model scale transfer in large complex systems, i.e. to model how low level of organization can be made to influence upper level and vice versa. This is a fundamental issue, and more particularly in ecological modeling where models are a real scientific tool of investigation. Individuals and populations are not described at the same scale of time and space but it is known that they act on each others. Based on this example, we model individuals in their environment and the population dynamics. While behavior is best modeled using an algorithmic framework (the reactive agent paradigm), population dynamics (because of the number of interacting entities) is best modeled using numerical models. We propose the use of the concept of emergent computation as a framework for coupling heterogeneous formalisms. In the same time, it is crucial to be aware of the consequences of the simplifications and of the choices that are made in the reactive agent model, such as the topology of space and various parameters. In this article, we discuss these issues and our approach on a case study drawn from marine ecology and we show that it is possible to find classical mathematical functional responses with a reactive agent system. Then, we propose a methodology to deal with the coupling of heterogeneous formalism useful in any kind of system modeling.
Oxygen stable isotope ratios of tree-ring cellulose: the next phase of understanding.

Summary Analysis of the oxygen isotope ratio of tree-ring cellulose is a valuable tool that can be used as a paleoclimate proxy. Our ability to use this tool has gone through different phases. The first began in the 1970s with the demonstration of empirical relationships between the oxygen isotope ratio of tree-ring cellulose and climate. These empirical relationships, however, did not provide us with the confidence that they are robust through time, across taxa and across geographical locations. The second phase began with a rudimentary understanding of the physiological and biochemical mechanisms responsible for the oxygen isotope ratios of cellulose, which is necessary to increase the power of this tool. This phase culminated in a mechanistic tree-ring model integrating concepts of physiology and biochemistry in a whole-plant system. This model made several assumptions about leaf water isotopic enrichment and biochemistry which, in the nascent third phase, are now being challenged, with surprising results. These third-phase results suggest that, contrary to the model assumption, leaf temperature across a large latitudinal gradient is remarkably constant and does not follow ambient temperature. Recent findings also indicate that the biochemistry responsible for the incorporation of the cellulose oxygen isotopic signature is not as simple as has been assumed. Interestingly, the results of these challenges have strengthened the tree-ring model. There are several other assumptions that can be investigated which will improve the utility of the tree-ring model.
HABITAT‐SPECIFIC SENSORY‐EXPLOITATIVE SIGNALS IN BIRDS: PROPENSITY OF DIPTERAN PREY TO CAUSE EVOLUTION OF PLUMAGE VARIATION IN FLUSH‐PURSUIT INSECTIVORES

Abstract Sensory exploitation occurs when signals trigger behavioral reactions that diminish the receiver's fitness. Research in this area focuses on the match between the signal's form and the receiver's sensitivity, but the effect of habitat on interspecific sensory exploitation is rarely addressed. Myioborus redstarts use conspicuous wing and tail displays of contrasting black‐and‐white plumage patches to flush dipteran insects, which are then pursued and captured in flight. Previous studies have shown that by increasing the distance at which insects perform an escape response, conspicuous visual displays improve the birds' foraging performance. We tested the hypothesis that selection for a visual signal that maximizes prey escape distance under local habitat conditions can lead to the evolution of geographic variation in plumage pattern among Myioborus redstarts. Using models of foraging birds, we recorded the escape responses of Dipterous insects to a range of plumage patterns and background tones (from light to dark) to determine whether the plumage pattern that maximizes prey flushing is dependent upon that habitat (background) against which birds are viewed by their prey. Our results indicate that the effectiveness of a particular plumage pattern in flushing dipteran prey depends strongly on the background against which that plumage pattern is displayed, and darker habitat (background) conditions generally favor plumages with more extensive patches of white in the tail. However, the addition of white wing patches that imitate the plumage of the painted redstart (Myioborus pictus) generally increases insect escape responses but reduces the effect that tail pattern variation and background tone have on escape behavior. These experiments support the hypothesis that habitat‐specific natural selection to enhance sensory exploitation of prey escape responses could produce geographic variation in plumage patterns of flush‐pursuers.
Main productive performance of Awassi sheep in the Central Anatolian Region of Turkey

This study aimed to determine milk yield, fertility, lamb growth, survival rate, and the effect of environmental factors on these parameters in the Awassi sheep of the Central Anatolian Region. The fertility parameters were determined to be as follows: heat rate, pregnancy rate, parturition rate, single-born rate, twinning rate, abortion rate, lamb rate, and number of lambs per parturition, based on the number of ewes assigned for mating, were 100%, 93.8%, 90.5%, 79.7%, 20.3%, 1.4%, 108.8%, and 1.20%, respectively. The survival rates of lambs at 60 and 120 days of age were 88.3% and 84.5%, respectively. The average lactation milk yield and lactation period of the Awassi ewes were 196.5 ± 5.60 kg and 184.3 ± 2.11 days, respectively. The general death and slaughter rate of the stock was 8.2% throughout the research period. The lactation milk yield was affected by the production year (P 0.05). The results of this study have shown that the Awassi sheep raised in the Central Anatolian Region had similar lactation milk yield, fertility parameters, and survival rates as the Awassi sheep’s original race. In addition, since there were no epidemic health problems observed during the 2-year research period, Awassi sheep were shown to be adapted to being raised in this region.
[Kinetic regulation of pre-messenger RNA alternative splicing].

Regulation cinetique de l’epissage alternatif des pre-ARN messagers : attention au ralentissement Gwendal Dujardin1, Alberto R. Kornblihtt2, Laurent Corcos3 1 Centre for Genomic Regulation, carrer Doctor Aiguader 88, 08003 Barcelona, Spain ; 2 Laboratorio de Fisiologia y Biologia Molecular, Departamento de Fisiologia, Biologia Molecular y Celular, IFIBYNE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellon 2, C1428EHA Buenos Aires, Argentine ; 3 Inserm U1078 equipe ECLA, Faculte de medecine, 22, avenue Camille Desmoulins, 29238 Brest Cedex 3, France. gwendal.dujardin@crg.eu ark@fbmc.fcen. uba.ar laurent.corcos@inserm.fr > Chez les eucaryotes, l’epissage alternatif est un mecanisme finement regule qui permet d’accroitre la complexite du proteome a partir d’un nombre limite de genes. En effet, le nombre de genes chez les vertebres n’est pas drastiquement different de celui qui est retrouve chez les invertebres (23 000 genes chez l’homme, 19 000 chez le ver C. elegans). La frequence de l’epissage alternatif augmentant des eucaryotes unicellulaires aux eucaryotes multicellulaires, celui-ci joue donc un role primordial dans la complexite des organismes. Chez les mammiferes, l’epissage alternatif affecte presque 95 % des genes [1]. La raison principale qui fait que l’epissage puisse etre alternatif est la force des sites bornant les exons en 5’ et en 3’, dictee par leur similitude a la sequence consensus, qui va determiner leur affinite pour des facteurs d’epissage et leur utilisation par la machinerie d’epissage. On parle alors de sites forts et de sites faibles et, en regle generale, lorsqu’un site d’epissage est fort, l’epissage est constitutif. La position relative de sites forts ou faibles va entrainer differents types d’epissage alternatif : inclusion/ exclusion d’exon, exclusion mutuelle d’exons, site d’epissage alternatif en 3’ ou en 5’ ou retention d’intron (les promoteurs multiples et les sites multiples de polyadenylation n’etant pas des evenements d’epissage alternatif au sens strict). L’utilisation d’un site faible d’epissage est influencee a la fois par des elements de regulation en cis et des facteurs trans qui se lient aux sequences cis-regulatrices, activatrices ou inhibitrices de l’epissage. Cependant, le taux d’inclusion d’un exon ne depend pas seulement de la force de ses sites d’epissage, de la presence de sequences cis-regulatrices ou de la concentration, ou des modifications du cancer, la fondation nationale danoise de recherche (DNRF82), le conseil medical de recherche, la fondation Novo Nordisk et le FP7 Marie Curie actions ITN nucleosome4D. La recherche dans le laboratoire de Juri Rappsilber est soutenue par le Wellcome Trust (084229, 077707, 092076, 091020). C.A a beneficie de bourses post doctorales EMBO, HFSP, du conseil medical de recherche danois et de l’ERC2011StG.