Miracle-dz/UniFAR-FTUs huggingface dataset:
Morphometric covariation between palatal shape and skeletal pattern in Class II growing subjects

Objectives To evaluate the patterns of covariation between palatal and craniofacial morphology in Class II subjects in the early mixed dentition by means of geometric morphometrics. Methods A cross-sectional sample of 85 Class II subjects (44 females, 41 males; mean age 8.7 years ± 0.8) was collected retrospectively according to the following inclusion criteria: European ancestry (white), Class II skeletal relationship, Class II division 1 dental relationship, early mixed dentition, and prepubertal skeletal maturation. Pre-treatment digital 3D maxillary dental casts and lateral cephalograms were available. Landmarks and semilandmarks were digitized (239 on the palate and 121 on the cephalogram) and geometric morphometric methods (GMM) were applied. Procrustes analysis and principal component analysis (PCA) were performed to reveal the main patterns of palatal shape and craniofacial skeletal shape variation. Two-block partial least squares analysis (PLS) assessed patterns of covariation between palatal morphology and craniofacial morphology. Results For the morphology of the palate, the first principal component (PC1) described variation in all three dimensions. For the morphology of the craniofacial complex, PC1 showed shape variation mainly in the vertical direction. Palatal shape and craniofacial shape covaried significantly (RV coefficient: 0.199). PLS1 accounted for more than 64 per cent of total covariation and related divergence of the craniofacial complex to palatal height and width. The more a Class II subject tended towards high-angle divergence, the narrower and higher was the palate. Conclusions Class II high-angle patients tended to have narrower and higher palates, while Class II low-angle patients were related to wider and more shallow palates.
Gender, Migration and HIV in Rural KwaZulu-Natal, South Africa

Objectives Research on migration and HIV has largely focused on male migration, often failing to measure HIV risks associated with migration for women. We aimed to establish whether associations between migration and HIV infection differ for women and men, and identify possible mechanisms by which women's migration contributes to their high infection risk. Design Data on socio-demographic characteristics, patterns of migration, sexual behavior and HIV infection status were obtained for a population of 11,677 women aged 15–49 and men aged 15–54, resident members of households within a demographic surveillance area participating in HIV surveillance in 2003–04. Methods Logistic regression was conducted to examine whether sex and migration were independently associated with HIV infection in three additive effects models, using measures of recent migration, household presence and migration frequency. Multiplicative effects models were fitted to explore whether the risk of HIV associated with migration differed for males and females. Further modeling and simulations explored whether composition or behavioral differences accounted for observed associations. Results Relative to non-migrant males, non-migrant females had higher odds of being HIV-positive (adjusted odds ratio [aOR] = 1.72; 95% confidence interval [1.49–1.99]), but odds were higher for female migrants (aOR = 2.55 [2.07–3.13]). Female migrants also had higher odds of infection relative to female non-migrants (aOR = 1.48 [1.23–1.77]). The association between number of sexual partners over the lifetime and HIV infection was modified by both sex and migrant status: For male non-migrants, each additional partner was associated with 3% higher odds of HIV infection (aOR = 1.03 [1.02–1.05]); for male migrants the association between number of partners and HIV infection was non-significant. Each additional partner increased odds of HIV infection by 22% for female non-migrants (aOR = 1.22 [1.12–1.32]) and 46% for female migrants (aOR = 1.46 [1.25–1.69]). Conclusions Higher risk sexual behavior in the context of migration increased women's likelihood of HIV infection.
ContextualNet: Exploiting Contextual Information Using LSTMs to Improve Image-Based Localization

Convolutional Neural Networks (CNN) have successfully been utilized for localization using a single monocular image [1]. Most of the work to date has either focused on reducing the dimensionality of data for better learning of parameters during training or on developing different variations of CNN models to improve pose estimation. Many of the best performing works solely consider the content in a single image, while the context from historical images is ignored. In this paper, we propose a combined CNN-LSTM which is capable of incorporating contextual information from historical images to better estimate the current pose. Experimental results achieved using a dataset collected in an indoor office space improved the overall system results to 0.8 m & 2.5° at the third quartile of the cumulative distribution as compared with 1.5 m & 3.0° achieved by PoseNet [1]. Furthermore, we demonstrate how the temporal information exploited by the CNN-LSTM model assists in localizing the robot in situations where image content does not have sufficient features. Keywords: Localization, Long Short Term Memory (LSTM), Computer Vision, Deep Neural Network, Pose estimation
CCR6, a CC Chemokine Receptor that Interacts with Macrophage Inflammatory Protein 3α and Is Highly Expressed in Human Dendritic Cells

Dendritic cells initiate immune responses by ferrying antigen from the tissues to the lymphoid organs for presentation to lymphocytes. Little is known about the molecular mechanisms underlying this migratory behavior. We have identified a chemokine receptor which appears to be selectively expressed in human dendritic cells derived from CD34+ cord blood precursors, but not in dendritic cells derived from peripheral blood monocytes. When stably expressed as a recombinant protein in a variety of host cell backgrounds, the receptor shows a strong interaction with only one chemokine among 25 tested: the recently reported CC chemokine macrophage inflammatory protein 3α. Thus, we have designated this receptor as the CC chemokine receptor 6. The cloning and characterization of a dendritic cell CC chemokine receptor suggests a role for chemokines in the control of the migration of dendritic cells and the regulation of dendritic cell function in immunity and infection.
Hippo-mediated suppression of IRS2/AKT signaling prevents hepatic steatosis and liver cancer

Nonalcoholic fatty liver disease (NAFLD) is a major risk factor for liver cancer; therefore, its prevention is an important clinical goal. Ablation of phosphatase and tensin homolog (PTEN) or the protein kinase Hippo signaling pathway induces liver cancer via activation of AKT or the transcriptional regulators YAP/TAZ, respectively; however, the potential for crosstalk between the PTEN/AKT and Hippo/YAP/TAZ pathways in liver tumorigenesis has thus far remained unclear. Here, we have shown that deletion of both PTEN and SAV1 in the liver accelerates the development of NAFLD and liver cancer in mice. At the molecular level, activation of YAP/TAZ in the liver of Pten–/– Sav1–/– mice amplified AKT signaling through the upregulation of insulin receptor substrate 2 (IRS2) expression. Both ablation of YAP/TAZ and activation of the Hippo pathway could rescue these phenotypes. A high level of YAP/ TAZ expression was associated with a high level of IRS2 expression in human hepatocellular carcinoma (HCC). Moreover, treatment with the AKT inhibitor MK-2206 or knockout of IRS2 by AAV-Cas9 successfully repressed liver tumorigenesis in Pten–/– Sav1–/– mice. Thus, our findings suggest that Hippo signaling interacts with AKT signaling by regulating IRS2 expression to prevent NAFLD and liver cancer progression and provide evidence that impaired crosstalk between these 2 pathways accelerates NAFLD and liver cancer.
Motions of leaves and stems, from growth to potential use

The study on aerial plant organs (leaves and stems) motions is reviewed. The history of observations and studies is put in the perspective of the ideas surrounding them, leading to a presentation of the current classification of these motions. After showing the shortcomings of such a classification, we present, following an idea of Darwin’s, the various movements in a renewed and observation-based perspective of the plant development. With this perspective, the different movements fit together logically, and in particular we point out that the mature reversible movements, such as the sensitive or circadian movements, are just partial regressions of the developmental ones.
WIsH: who is the host? Predicting prokaryotic hosts from metagenomic phage contigs

Summary: WIsH predicts prokaryotic hosts of phages from their genomic sequences. It achieves 63% mean accuracy when predicting the host genus among 20 genera for 3 kbp‐long phage contigs. Over the best current tool, WisH shows much improved accuracy on phage sequences of a few kbp length and runs hundreds of times faster, making it suited for metagenomics studies. Availability and implementation: OpenMP‐parallelized GPL‐licensed C ++ code available at https://github.com/soedinglab/wish. Contact: clovis.galiez@mpibpc.mpg. de or soeding@mpibpc.mpg. de Supplementary information: Supplementary data are available at Bioinformatics online.
Monitoring of cerebral oximetry during head-up tilt test in adults with history of syncope and orthostatic intolerance

Aims We applied near-infrared-spectroscopy (NIRS) to measure absolute frontal cerebral tissue oxygen saturation (SctO2) during head-up tilt test (HUT) in patients investigated for unexplained syncope. Methods and results Synchronized non-invasive beat-to-beat haemodynamic monitoring, ECG, SctO2 (NIRS; normal range: 60-80%), and peripheral oxygen saturation (left hand, SpO2) were applied during HUT in a random sample of patients with unexplained syncope. Tracings of 54 patients (mean-age: 55 ± 19 years, 39% male) with negative HUT, vasovagal syncope (VVS), or orthostatic hypotension (OH) were analysed. In 44 patients HUT was diagnostic, in 10 HUT was negative. Thirty-one experienced VVS. Of these, 6 had spontaneous and 25 nitroglycerin-induced syncope. Thirteen patients had orthostatic hypotension (OH). Although there was no significant change in mean-arterial pressure from baseline to 1 min before syncope or end of passive HUT phase (-1.4 ± 13.9 mmHg; P = 0.45), there was a significant fall in SctO2 during the same period (-3.2 ± 3.2%; P ≤ 0.001). Among patients who experienced syncope, a decrease in SctO2 from 71 ± 5% at baseline to 53 ± 9% (P < 0.001) at syncope was observed. During HUT, there was a significant difference in delta SctO2 between spontaneous VVS (-4.5 ± 3.0%) and negative HUT (-1.3 ± 1.9%; P = 0.021), but not between spontaneous VVS and OH (-5.4 ± 4.2%; P = 0.65). In spontaneous VVS, progressive decrease of SctO2 was independent of mean arterial pressure decrease (P = 0.22). Conclusions Progressive decrease in cerebral tissue oxygenation independent of mean-arterial pressure may precede spontaneous vasovagal reflex during tilt. Patients experience syncope when SctO2 falls below 60%. These data confirm clinical utility of absolute cerebral oximetry monitoring for syncope investigation. We applied NIRS to measure frontal cerebral tissue oxygen saturation (SctO2) during head-up tilt test (HUT) in patients with unexplained syncope. In 44 of 54 patients, HUT was diagnostic. In patients with syncope, a significant SctO2-decrease was observed. Different patterns of SctO2 can be detected.
Oxytocin Reduces Cocaine Cued Fos Activation in a Regionally Specific Manner

Abstract Background Oxytocin may be a possible treatment for multiple neuropsychiatric disorders, including cocaine addiction. Little is known about the site-specific effects of oxytocin on various drug addiction-related brain regions. Furthermore, sexually dimorphic effects of oxytocin on neural function in the addiction circuit have not been established. Here, we studied Fos expression following cocaine-cued reinstatement in both male and female rats. Methods Male and female rats underwent self-administration, extinction, and reinstatement tests. On test days, rats were given oxytocin or vehicle, and lever pressing was measured in response to conditioned cocaine cues. Rats were perfused and Fos staining measured in the central amygdala, medial prefrontal cortex, nucleus accumbens core, and subthalamic nucleus. Fos/oxytocin double labeling occurred in the paraventricular nucleus of the hypothalamus. Results Rats reinstated to cocaine cues relative to extinction responding and oxytocin reduced cocaine seeking. Oxytocin combined with contingent cue presentations increased Fos+ oxytocin cell bodies within the paraventricular nucleus of the hypothalamus relative to vehicle. Fos expression robustly increased in the central amygdala following oxytocin administration. Oxytocin reversed cue-induced Fos expression in the medial prefrontal cortex, nucleus accumbens core, and subthalamic nucleus. Central oxytocin infusion also attenuated reinstated cocaine seeking. Conclusions Oxytocin decreased reinstated cocaine seeking, increased Fos activation in the paraventricular nucleus of the hypothalamus and central amygdala, but normalized cue-induced Fos activation in the medial prefrontal cortex, nucleus accumbens core, and subthalamic nucleus, thereby demonstrating regionally specific activation patterns. No sex differences were seen for the effects of oxytocin on cocaine seeking and Fos activation, indicating that oxytocin acts on similar central neural circuits critical to reinstated cocaine seeking in both males and females.
Efficacy of postoperative radiotherapy in patients with pathological stage N2 epidermal growth factor receptor wild type adenocarcinoma and squamous cell carcinoma lung cancer

Purpose Few large, prospective, randomized studies have compared the effects of postoperative radiotherapy (PORT) in pathological N2 (pN2) with those of surgical resection alone. in terms of long-term survival in lung adenocarcinoma (adenoCA; wild-type [WT] epidermal growth factor receptor [EGFR]) and squamous cell carcinoma (squCA) settings. This nationwide cohort study clarifies the role of PORT in the survival of pN2 lung adenoCA (WT EGFR) and squCA patients Patients and Methods We analyzed data of patients with adenoCA (WT EGFR) and squCA collected from the Taiwan Cancer Registry database. The patients were categorized into five groups according to the treatment modality: Group 1 (surgery alone), Group 2 (adjuvant chemotherapy [CT] alone), Group 3 (adjuvant radiotherapy [RT] alone), Group 4 (adjuvant concurrent chemoradiotherapy [CCRT]), and Group 5 (adjuvant sequential CT and intensity-modulated RT [IMRT]). Results We enrolled 588 lung adenoCA (WT EGFR) and squCA patients without distant metastasis. After adjustments for age at surgery, surgical years, and Charlson comorbidity index scores, the multivariate Cox regression analysis demonstrated that adjusted HRs (aHRs; 95% confidence intervals [CIs]) for the overall mortality of female lung adenoCA (WT EGFR) patients were 0.257 (0.111-0.594), 0.530 (0.226-1.243), 0.192 (0.069-0.534), and 0.399 (0.172-0.928) in Groups 2, 3, 4, and 5, respectively. For male lung squCA patients, the aHRs (95% CIs) for overall mortality were 0.269 (0.160-0.451), 0.802 (0.458-1.327), 0.597 (0.358-0.998), and 0.456 (0.265-0.783) in Groups 2, 3, 4, and 5, respectively. Conclusions Adjuvant CCRT or sequential CT and IMRT at ≥5000 cGy significantly reduced the mortality rate of female lung adenoCA (WT EGFR) and male squCA pN2 patients.
Interferon-Alpha Mediates Restriction of Human Immunodeficiency Virus Type-1 Replication in Primary Human Macrophages at an Early Stage of Replication

Type I interferons (IFNα and β) are induced directly in response to viral infection, resulting in an antiviral state for the cell. In vitro studies have shown that IFNα is a potent inhibitor of viral replication; however, its role in HIV-1 infection is incompletely understood. In this study we describe the ability of IFNα to restrict HIV-1 infection in primary human macrophages in contrast to peripheral blood mononuclear cells and monocyte-derived dendritic cells. Inhibition to HIV-1 replication in cells pretreated with IFNα occurred at an early stage in the virus life cycle. Late viral events such as budding and subsequent rounds of infection were not affected by IFNα treatment. Analysis of early and late HIV-1 reverse transcripts and integrated proviral DNA confirmed an early post entry role for IFNα. First strand cDNA synthesis was slightly reduced but late and integrated products were severely depleted, suggesting that initiation or the nucleic acid intermediates of reverse transcription are targeted. The depletion of integrated provirus is disproportionally greater than that of viral cDNA synthesis suggesting the possibility of a least an additional later target. A role for either cellular protein APOBEC3G or tetherin in this IFNα mediated restriction has been excluded. Vpu, previously shown by others to rescue a viral budding restriction by tetherin, could not overcome this IFNα induced effect. Determining both the viral determinants and cellular proteins involved may lead to novel therapeutic approaches. Our results add to the understanding of HIV-1 restriction by IFNα.
Genetic assessment for the endangered black lion tamarin Leontopithecus chrysopygus (Mikan, 1823), Callitrichidae, Primates

This is the first study analyzing genetic diversity in captive individuals of the endangered black lion tamarin, Leontopithecus chrysopygus, and also comparing genetic diversity parameters between wild populations and captive groups using the same set of molecular markers. We evaluated genetic diversity and differentiation for the Brazilian and European captive groups and a wild population through 15 polymorphic microsatellite markers. The genetic diversity levels were similar among Brazilian captive, European captive and wild animals from the National Forest of Capão Bonito. Expected heterozygosity showed values ranging from 0.403 to 0.462, and significant differences were not observed among the populations. Different allele frequencies were observed among the groups, which showed the presence of distinct private alleles. The PCoA analysis evidenced three main clusters suggesting that the captive Brazilian and European groups are markedly differentiated both from one another and from the wild population of Capão Bonito. Likewise, the most likely number of genetic clusters (K) revealed by Structure was three. Such a structure is probably the result of the strength of drift and non‐random reproduction in these small and isolated groups. Despite this differentiation, all groups still have similar genetic diversity levels, comparable to other callitrichids. The data obtained herein are important to increasing knowledge of the genetics of tamarins and supporting breeding programs to prevent loss of genetic diversity and inbreeding depression.
Icephobic Material Centrifuge Adhesion Test

Ice accumulation is a transportation problem for roads, boats, airplanes transmission lines, etc. An icephobic coating applied to exposed surfaces appears to be an interesting solution to prevent ice build-up; however, no coating is perfectly icephobic as ice sticks to everything. Still, some materials that reduce ice adhesion have been developed from which the ice can be more easily shed, possibly even with existing forces such as wind, gravity and vibrations. A method was therefore investigated to measure the ice adhesion and the reduction thereof. The method must be able to measure the force required to separate the ice from the substrate, i.e. adhesive failure and be a comparative method. Existing tests use traction or compressive forces, however, for such, the ice can only be made by freezing water as a block which leads to highly variable results: up to 300% error. To solve these limitations the Anti-icing Material International Laboratory (AMIL) developed the Centrifuge Adhesion Test. The test involves icing the extremity of small beams under supercooled precipitation. After icing, the beams are balanced in a centrifuge and rotated at an accelerating speed until the ice detaches. The ice detachment is picked up by piezoelectric cells located in the vat wall. The ice adhesion shear stress is then calculated from the ice detachment rotation speed. The results are then reported as an Adhesion Reduction Factor, which is the ratio of the adhesion shear stress of the beams with a candidate coating with respect to a simultaneously iced uncoated beam. Therefore, a bare beam would have a factor of one, the higher the factor the more icephobic the coating and values below one indicate and increase in adhesion. The advantages of this method include: the fact that the ice is made from supercooled precipitation and is representative# of atmospheric icing; the small ice samples allow for a homogeneous ice coupon which improves the repeatability of the results; the flat ice surface allows for modifications to the shape of the surface (e.g. cylinders and airfoils) and exposure of the surface to environmental elements.
Inference with model uncertainty on indoor scene for semantic segmentation

This paper presents a novel semantic segmentation method using model uncertainty on indoor scene. Recently, deep convolutional encoder-decoder neural networks achieved good segmentation performance and we also implement this network. Toward practical use of the semantic segmentation, it is necessary to recognize accurately whether the object is known or not. However, many architectures do not consider an uncertainty of the segmentation result. Bayesian SegNet enables it to produce an uncertainty of the segmentation results with a measure of model uncertainty but the uncertainty is not used for segmentation itself. Our study aims the improvement of classification accuracy for semantic segmentation in indoor scene understanding using model uncertainty. Therefore, we use SUN RGB-D indoor scene dataset for the training and testing of our network. Our method rejects the uncertain region and classifies it as an unknown object using the model uncertainty. As a result, we succeeded in reducing wrong predictions. Furthermore, our method showed good classification performance in the comparison with other architectures such as FCN, SegNet, Bayesian SegNet, and so on. We achieved improvement of classification accuracy by our method as shown in the evaluation results.
Fault Injection Modeling Attacks on 65 nm Arbiter and RO Sum PUFs via Environmental Changes

Physically Unclonable Functions (PUFs) are emerging as hardware security primitives. So-called strong PUFs provide a mechanism to authenticate chips which is inherently unique for every manufactured sample. To prevent cloning, modeling of the challenge-response pair (CRP) behavior should be infeasible. Machine learning (ML) algorithms are a well-known threat. Recently, repeatability imperfections of PUF responses have been identified as another threat. CMOS device noise renders a significant fraction of the CRPs unstable, hereby providing a side channel for modeling attacks. In previous work, 65 nm arbiter PUFs have been modeled as such with accuracies exceeding 97%. However, more PUF evaluations were required than for state-of-the-art ML approaches. In this work, we accelerate repeatability attacks by increasing the fraction of unstable CRPs. Response evaluation faults are triggered via environmental changes hereby. The attack speed, which is proportional to the fraction of unstable CRPs, increases with a factor 2.4 for both arbiter and ring oscillator (RO) sum PUFs. Data originates from a 65 nm silicon chip and hence not from simulations.