Miracle-dz/UniFAR-FTUs huggingface dataset:
Differentiating Dental Pulp Cells via RGD-Dendrimer Conjugates

Traumatic dental injuries are often irreversible, underscoring the need for therapies that protect dental pulp cells and enhance their regeneration. We hypothesized that generation 5 poly amido amine (PAMAM) dendrimers (G5), functionalized with fluorescein isothiocyanate (FL) and αVβ3-specific, cyclic arginine-glycine-aspartic acid (RGD) peptides, will bind to dental pulp cells (DPCs) and modulate their differentiation. Dental pulp cells and mouse odontoblast-like cells (MDPC-23) (±) treated with G5-FL-RGD were analyzed via Western blot, RT-PCR, and quantitative PCR. Transcription of dental differentiation markers was as follows: Dentin matrix protein (DMP-1), dentin sialoprotein (DSPP), and matrix extracellular phosphoglycoprotein (MEPE) as well as vascular endothelial growth factor (VEGF) all increased via the JNK pathway. Long-term G5-RGD treatment of dental pulp cells resulted in enhanced mineralization as examined via Von Kossa assay, suggesting that PAMAM dendrimers conjugated to cyclic RGD peptides can increase the odontogenic potential of these cells.
Specifying a Realistic File System

We present the most interesting elements of the correctness specification of BilbyFs, a performant Linux flash file system. The BilbyFs specification supports asynchronous writes, a feature that has been overlooked by several file system verification projects, and has been used to verify the correctness of BilbyFs’s fsync() C implementation. It makes use of nondeterminism to be concise and is shallowly-embedded in higher-order logic.
Validation of the ALS Assay in Adult Patients with Culture Confirmed Pulmonary Tuberculosis

Background We have earlier shown that Bacille Calmette-Guérin (BCG) vaccine-specific IgG Antibodies in Lymphocyte Supernatant (ALS) can be used for diagnosis of active tuberculosis (TB) in adults and children. Methodology/Principal Findings The ALS method was validated in a larger cohort (n = 212) of patients with suspicion of pulmonary TB using multiple antigens (BCG, LAM, TB15.3, TB51A, CFP10-ESAT6-A, CFP, CW) from Mycobacterium tuberculosis. The sensitivity and specificity of the ALS assay was calculated using non-TB patients as controls. The sensitivity and the specificity were highest with BCG vaccine (90% and 88% respectively) followed by LAM (89% and 87% respectively). Simultaneous assessment of multiple antigen-specific antibodies increased sensitivity (91%) and specificity (88%). Using higher lymphocyte count in smaller volume of culture media increased detection and reduced the assay duration to ∼30 hrs. Twenty one patients with clinical findings strongly suggestive of TB finally diagnosed as non-TB patients were positive by the ALS assay, of which 9 (43%) were positive for 7 antigens and 19 (90%) for at least 3 antigens. Conclusions/Significance Our findings show that simultaneous detection of antigens improves the diagnostic potential of the ALS assay; the modified method increases sensitivity and can provide results in <48 hours, and enable detection of some cases of pulmonary TB that are not detectable by standard methods.
Posterior calibration and exploratory analysis for natural language processing models

Many models in natural language processing define probabilistic distributions over linguistic structures. We argue that (1) the quality of a model' s posterior distribution can and should be directly evaluated, as to whether probabilities correspond to empirical frequencies, and (2) NLP uncertainty can be projected not only to pipeline components, but also to exploratory data analysis, telling a user when to trust and not trust the NLP analysis. We present a method to analyze calibration, and apply it to compare the miscalibration of several commonly used models. We also contribute a coreference sampling algorithm that can create confidence intervals for a political event extraction task.
Upregulation of CREB-Mediated Transcription Enhances Both Short- and Long-Term Memory

Unraveling the mechanisms by which the molecular manipulation of genes of interest enhances cognitive function is important to establish genetic therapies for cognitive disorders. Although CREB is thought to positively regulate formation of long-term memory (LTM), gain-of-function effects of CREB remain poorly understood, especially at the behavioral level. To address this, we generated four lines of transgenic mice expressing dominant active CREB mutants (CREB-Y134F or CREB-DIEDML) in the forebrain that exhibited moderate upregulation of CREB activity. These transgenic lines improved not only LTM but also long-lasting long-term potentiation in the CA1 area in the hippocampus. However, we also observed enhanced short-term memory (STM) in contextual fear-conditioning and social recognition tasks. Enhanced LTM and STM could be dissociated behaviorally in these four lines of transgenic mice, suggesting that the underlying mechanism for enhanced STM and LTM are distinct. LTM enhancement seems to be attributable to the improvement of memory consolidation by the upregulation of CREB transcriptional activity, whereas higher basal levels of BDNF, a CREB target gene, predicted enhanced shorter-term memory. The importance of BDNF in STM was verified by microinfusing BDNF or BDNF inhibitors into the hippocampus of wild-type or transgenic mice. Additionally, increasing BDNF further enhanced LTM in one of the lines of transgenic mice that displayed a normal BDNF level but enhanced LTM, suggesting that upregulation of BDNF and CREB activity cooperatively enhances LTM formation. Our findings suggest that CREB positively regulates memory consolidation and affects memory performance by regulating BDNF expression.
Monitoring Linked Epidemics: The Case of Tuberculosis and HIV

Background The tight epidemiological coupling between HIV and its associated opportunistic infections leads to challenges and opportunities for disease surveillance. Methodology/Principal Findings We review efforts of WHO and collaborating agencies to track and fight the TB/HIV co-epidemic, and discuss modeling—via mathematical, statistical, and computational approaches—as a means to identify disease indicators designed to integrate data from linked diseases in order to characterize how co-epidemics change in time and space. We present R TB/HIV, an index comparing changes in TB incidence relative to HIV prevalence, and use it to identify those sub-Saharan African countries with outlier TB/HIV dynamics. R TB/HIV can also be used to predict epidemiological trends, investigate the coherency of reported trends, and cross-check the anticipated impact of public health interventions. Identifying the cause(s) responsible for anomalous R TB/HIV values can reveal information crucial to the management of public health. Conclusions/Significance We frame our suggestions for integrating and analyzing co-epidemic data within the context of global disease monitoring. Used routinely, joint disease indicators such as R TB/HIV could greatly enhance the monitoring and evaluation of public health programs.
Preorogenic exhumation of the North Pyrenean Agly massif (Eastern Pyrenees‐France)

The Pyrenees, north of the North Pyrenean fault, display a complex structure involving a succession of peridotite massifs, basement massifs, and mid‐Cretaceous to Late Cretaceous basins located in a narrow domain, which was affected by a mid‐Cretaceous, preorogenic, high‐temperature, low‐pressure metamorphism. The Late Cretaceous basins were interpreted either as pull‐apart basins formed during transcurrent motion of Iberia relative to Eurasia or as remnants of a larger extensional basin. Recent models support that peridotite massifs result from the exhumation of the mantle during this preorogenic event. The northern boundary of the Agly basement massif shows evidence of ductile deformation of the basal formations of the Agly sedimentary cover. Macroscopic and microscopic kinematics indicators consistent with asymmetry of crystallographic fabrics suggest normal sense of shear and thus suggest detachment, at least partial, of the Mesozoic cover from its basement. Triassic to Early Cretaceous limestones are mylonitic and consistently shows a foliation, a NS‐ to NE‐trending lineation, shear criteria suggesting top‐to‐the‐north shearing and locally boudinage. At the microscopic scale, mylonites are characterized by a very fine grain size, frequently <10 µm. They contain larger, partially recrystallized calcite parent grains and undeformed quartz grains with calcite fringes crystallized in pressure shadows. In these mylonites, calcite systematically shows a weak but well‐defined crystallographic‐preferred orientations, suggesting HT dislocation creep combined to diffusion creep and possibly grain boundary sliding in the finest fraction of the mylonites. Paleotemperatures determined using Raman spectrometry suggest synkinematic temperature conditions in the range 340–390°C, in good agreement with observed microstructures and calcite CPO. The mylonitic fabric in Mesozoic limestones is folded by EW‐trending Pyrenean folds north of the Agly basement massif, attesting that this fabric formed before the Pyrenean orogeny. These data consistently support preorogenic extension under medium‐temperature conditions of the northern Agly massif and likely of the massif itself. Since simultaneously (~100 Ma) a mid‐Cretaceous basin opened south of the basement massif, we suggest a model of preorogenic exhumation of the Agly massif in response to the regional extension associated to the rotation of Iberia. This model may explain the exhumation of the North Pyrenean massifs during a single preorogenic event that allowed the opening of extensional basins and the exhumation of the lithospheric mantle. All these structures being subsequently reworked during the Pyrenean orogeny.
The Influence of Tobacco Smoke on Protein and Metal Levels in the Serum of Women during Pregnancy

Background Tobacco smoking by pregnant women has a negative effect on fetal development and increases pregnancy risk by changing the oxidative balance and microelements level. Smoking affects the concentration, structure and function of proteins, potentially leading to various negative effects on pregnancy outcomes. Methodology/Principal Findings The influence of tobacco smoke on key protein fractions in smoking and non-smoking healthy pregnant women was determined by capillary electrophoresis (CE). Concentrations of the proteins α1-antitrypsin, α1-acid glycoprotein, α2-macroglobulin and transferrin were determined by ELISA tests. Total protein concentration was measured by the Biuret method. Smoking status was established by cotinine levels. Cadmium (Cd) and Zinc (Zn) concentrations were determined by flame atomic absorption spectrometry and the Zn/Cd ratio was calculated based on these numbers. Smoking women had a 3.7 times higher level of Cd than non-smoking women. Zn levels decreased during pregnancy for all women. The Zn/Cd ratio was three times lower in smoking women. The differences between the changes in the protein profile for smoking and non-smoking women were noted. Regarding proteins, α1-antitrypsin and α2-macroglobulin levels were lower in the non-smoking group than in the smoking group and correlated with Cd levels (r = -0.968, p = 0.032 for non-smokers; r = −0.835, p = 0.019 for smokers). Zn/Cd ratios correlated negatively with α1-, α2- and β-globulins. Conclusions/Significance Exposure to tobacco smoke increases the concentration of Cd in the blood of pregnant women and may lead to an elevated risk of pregnancy disorders. During pregnancy alter concentrations of some proteins. The correlation of Cd with proteins suggests that it is one of the causes of protein aberrations.
Physical activity counseling by primary care physicians: attitudes, knowledge, implementation, and perceived success.

BACKGROUND In physical activity (PA) counseling, primary care physicians (PCPs) play a key role because they are in regular contact with large sections of the population and are important contact people in all health-related issues. However, little is known about their attitudes, knowledge, and perceived success, as well as about factors associated with the implementation of PA counseling. METHODS We collected data from 4074 PCPs including information on physician and practice characteristics, attitudes toward cardiovascular disease (CVD) prevention, and measures used during routine practice to prevent CVD. Here, we followed widely the established 5 A's strategy (Assess, Advise, Agree, Assist, Arrange). RESULTS The majority (87.2%) of PCPs rated their own level of competence in PA counseling as 'high,' while 52.3% rated their own capability to motivate patients to increase PA as 'not good. ' Nine of ten PCPs routinely provided at least 1 measure of the modified 5 A's strategy, while 9.5% routinely used all 5 intervention strategies. CONCLUSIONS The positive attitude toward PA counseling among PCPs should be supported by other stakeholders in the field of prevention and health promotion. An example would be the reimbursement of health counseling services by compulsory health insurance, which would enable PCPs to invest more time in individualized health promotion.
The Nematode Pristionchus pacificus (Nematoda: Diplogastridae) Is Associated with the Oriental Beetle Exomala orientalis (Coleoptera: Scarabaeidae) in Japan

Abstract Pristionchus pacificus has been developed as a nematode satellite organism in evolutionary developmental biology. Detailed studies of vulva development revealed multiple differences in genetic and molecular control in P. pacificus compared to the model organism Caenorhabditis elegans. To place evolutionary developmental biology in a comprehensive evolutionary context, such studies have to be complemented with ecology. In recent field studies in western Europe and eastern North America we found 11 Pristionchus species that are closely associated with scarab beetles and the Colorado potato beetle. However, P. pacificus was not commonly found in association with scarab beetles in these studies. Here, we describe the results of a similar survey of scarab beetles in Japan. Pristionchus pacificus was the most common Pristionchus species on scarab beetles in Japan, with 40 out of 43 (93%) isolates. The other Pristionchus isolates represent three novel species, which we refer to as Pristionchus sp. 11, Pristionchus sp. 14, and Pristionchus sp. 15. Thirty-seven of the established P. pacificus strains were found on the oriental beetle Exomala orientalis. Laboratory studies with the sex pheromone (Z)-7-tetradecen-2-one of the oriental beetle revealed that P. pacificus shows strong olfactory attraction to the beetle's sex pheromone, which provides a potential mechanism for the recognition and interaction of P. pacificus and E. orientalis. Together, this study identifies P. pacificus as the most common Pristionchus nematode in field studies in Japan, identifies E. orientalis as an important host species, and provides the basis for the ecology of P. pacificus.
Automated runtime recovery for QoS-based service composition

Service composition uses existing service-based applications as components to achieve a business goal. The composite service operates in a highly dynamic environment; hence, it can fail at any time due to the failure of component services. Service composition languages such as BPEL provide a compensation mechanism to rollback the error. But such a compensation mechanism has several issues. For instance, it cannot guarantee the functional properties of the composite service after compensation. In this work, we propose an automated approach based on a genetic algorithm to calculate the recovery plan that could guarantee the satisfaction of functional properties of the composite service after recovery. Given a composite service with large state space, the proposed method does not require exploring the full state space of the composite service; therefore, it allows efficient selection of recovery plan. In addition, the selection of recovery plans is based on their quality of service (QoS). A QoS-optimal recovery plan allows effective recovery from the state of failure. Our approach has been evaluated on real-world case studies, and has shown promising results.
Assessment of Predictive Markers for Placental Inflammatory Response in Preterm Births

Placental inflammatory response (PIR) is associated with adverse neonatal outcomes such as sepsis, cerebral palsy, low birth weight, preterm birth, and neonatal mortality. However, there is an urgent need for noninvasive and sensitive biomarkers for prediction of PIR. In this study, we evaluated the clinical usefulness of maternal serum inflammatory markers for prediction of PIR in women with impending preterm birth. We conducted a retrospective cohort study of 483 patients who delivered preterm neonates. Serum levels of leukocyte differential counts, C-reactive protein (CRP), and neutrophil to lymphocyte ratio (NLR) were compared between women with no placental inflammation and women with PIR. The mean neutrophil counts, CRP levels, and NLR in both the patients with histologic chorioamnionitis (HCA) alone and those with HCA with funisitis were significantly higher than those in women with no placental inflammation. Compared to leukocyte subset or CRP, NLR in women with funisitis was significantly higher than in women with HCA alone and showed higher predictive accuracy, along with 71.4% sensitivity, 77.9% specificity, 80.7% positive predictive value, and 67.8% negative predictive value for prediction of PIR. On Kaplan-Meier survival analysis, women with both an elevated level of CRP and a high NLR had a shorter admission-to-delivery interval compared to women with either an elevated level of CRP or a high NLR alone. NLR may be a predictive marker of PIR and could be used as a cost-effective parameter for identifying women at risk of PIR.
The off-shell Veneziano amplitude in Schnabl gauge

We give a careful definition of the open string propagator in Schnabl gauge and present its worldsheet interpretation. The propagator requires two Schwinger parameters and contains the BRST operator. It builds surfaces by gluing strips of variable width to the left and to the right of off-shell states with contracted or expanded local frames. We evaluate explicitly the four-point amplitude of off-shell tachyons. The computation involves a subtle boundary term, crucial to enforce the correct exchange symmetries. Interestingly, the familiar on-shell physics emerges even though string diagrams produce Riemann surfaces more than once. Off-shell, the amplitudes do not factorize over intermediate on-shell states.
A comparative study of the vascularization of the adrenal gland in the rabbit, rat and cat.

The work of Gerard (1913) and Anson, Cauldwell, Pick & Beaton (1947) has given a new insight into the vascularization of the human adrenal gland. While the source of the adrenal arteries from the inferior phrenic artery, aorta and renal artery, as described in contemporary textbooks of anatomy, is well known, it is not generally appreciated that the arteries from each source divide on approaching the adrenal, so that fifty or more arteries are to be found entering the periphery of the gland. Yet there is only one vein leaving it, which for the greater part of its length has only longitudinal smooth muscle in its coat (Brunn, 1873; Ferguson, 1906; Bargmann, 1933; Velican, 1948). This vascular arrangement is one which seems to be well fitted for ensuring an efficient blood flow through the adrenal. It is therefore important to assess the area of distribution of the arteries within the gland and the degree of anastomosis between them, for the efficiency of the arterial supply will depend on the functional capacity of this anastomosis. Hoerr (1931) claimed that if all the blood vessels to the guinea-pig adrenal are lightly ligatured the gland atrophies fairly rapidly, being replaced by connective tissue at the end of 3 months. He observed, however, that if only the main blood vessels are ligatured, without disturbing any small capsular anastomoses, blood vessels from the latter will canalize the degenerating parenchymatous tissue so that the adrenal presents a surprising resemblance to the normal gland at the end of 3 months; but many cells fuse with their neighbours to form giant cells of fifty or more nuclei. Vogt (1947), in denervation of the rat adrenal, found it impossible to avoid injury to an artery; a small infarct at the cranial surface of the gland invariably resulted, and occasionally even atrophy of the whole gland. Since these two observations are no more than occasional findings made in the course of other investigations, and pay no attention to the site of origin of the arteries interrupted or to their distribution within the gland, itwas decided to examine first the detailed vascularization of the adrenal in one animal, the rabbit, and to determine the result of interruption of individual arteries. Subsequently a comparative study was made, under similar conditions, of the cat and the rat.
Visuotopic Cortical Connectivity Underlying Attention Revealed with White-Matter Tractography

Visual attention selects behaviorally relevant information for detailed processing by resolving competition for representation among stimuli in retinotopically organized visual cortex. The signals that control this attentional biasing are thought to arise in a frontoparietal network of several brain regions, including posterior parietal cortex. Recent studies have revealed a topographic organization in the intraparietal sulcus (IPS) that mirrors the retinotopic organization in visual cortex, suggesting that connectivity between these regions might provide the mechanism by which attention acts on early cortical representations. Using white-matter imaging and functional MRI, we examined the connectivity between two topographic regions of IPS and six retinotopically defined areas in visual cortex. We observed a strong positive correlation between attention modulations in visual cortex and connectivity of posterior IPS, suggesting that these white-matter connections mediate the attention signals that resolve competition among stimuli for representation in visual cortex. Furthermore, we found that connectivity between IPS and V1 consistently respects visuotopic boundaries, whereas connections to V2 and V3/VP disperse by 60%. This pattern is consistent with changes in receptive field size across regions and suggests that a primary role of posterior IPS is to code spatially specific visual information. In summary, we have identified white-matter pathways that are ideally suited to carry attentional biasing signals in visuotopic coordinates from parietal control regions to sensory regions in humans. These results provide critical evidence for the biased competition theory of attention and specify neurobiological constraints on the functional brain organization of visual attention.
Chemophoresis as a driving force for intracellular organization: Theory and application to plasmid partitioning

Biological units such as macromolecules, organelles, and cells are directed to a proper location by gradients of chemicals. We consider a macroscopic element with surface binding sites where chemical adsorption reactions can occur and show that a thermodynamic force generated by chemical gradients acts on the element. By assuming local equilibrium and adopting the grand potential used in thermodynamics, we derive a formula for the “chemophoresis” force, which depends on chemical potential gradients and the Langmuir isotherm. The conditions under which the formula is applicable are shown to occur in intracellular reactions. Further, the role of the chemophoresis in the partitioning of bacterial chromosomal loci/plasmids during cell division is discussed. By performing numerical simulations, we demonstrate that the chemophoresis force can contribute to the regular positioning of plasmids observed in experiments.