Miracle-dz/UniFAR-FTUs huggingface dataset:
Bacterial Surface Appendages Strongly Impact Nanomechanical and Electrokinetic Properties of Escherichia coli Cells Subjected to Osmotic Stress

The physicochemical properties and dynamics of bacterial envelope, play a major role in bacterial activity. In this study, the morphological, nanomechanical and electrohydrodynamic properties of Escherichia coli K-12 mutant cells were thoroughly investigated as a function of bulk medium ionic strength using atomic force microscopy (AFM) and electrokinetics (electrophoresis). Bacteria were differing according to genetic alterations controlling the production of different surface appendages (short and rigid Ag43 adhesins, longer and more flexible type 1 fimbriae and F pilus). From the analysis of the spatially resolved force curves, it is shown that cells elasticity and turgor pressure are not only depending on bulk salt concentration but also on the presence/absence and nature of surface appendage. In 1 mM KNO3, cells without appendages or cells surrounded by Ag43 exhibit large Young moduli and turgor pressures (∼700–900 kPa and ∼100–300 kPa respectively). Under similar ionic strength condition, a dramatic ∼50% to ∼70% decrease of these nanomechanical parameters was evidenced for cells with appendages. Qualitatively, such dependence of nanomechanical behavior on surface organization remains when increasing medium salt content to 100 mM, even though, quantitatively, differences are marked to a much smaller extent. Additionally, for a given surface appendage, the magnitude of the nanomechanical parameters decreases significantly when increasing bulk salt concentration. This effect is ascribed to a bacterial exoosmotic water loss resulting in a combined contraction of bacterial cytoplasm together with an electrostatically-driven shrinkage of the surface appendages. The former process is demonstrated upon AFM analysis, while the latter, inaccessible upon AFM imaging, is inferred from electrophoretic data interpreted according to advanced soft particle electrokinetic theory. Altogether, AFM and electrokinetic results clearly demonstrate the intimate relationship between structure/flexibility and charge of bacterial envelope and propensity of bacterium and surface appendages to contract under hypertonic conditions.
A recent survey for human activity recoginition based on deep learning approach

Human activity recognition is an active research topic in computer vision due to its applicability to wide range of application areas such as smart surveillance, robot learning, human computer interaction, health assessment. Identifying human activities from video sequences constitutes one of the most challenging tasks in the field of computer vision, especially due to the harsh nature of the real-world activity recognition scenarios and high volumes of data that need to be worked upon. The techniques available in the literature for activity recognition are broadly classified into two categories: single layered approaches aimed at recognition of much simpler activities, hierarchical approaches aimed at recognition of complex activities in terms of simpler ones. Deep learning is one of the hierarchical approaches for recognizing human activities capable of achieving outstanding results and outperforming other "non-deep" state-of-the-art methods by effectively utilizing the image structure in reducing the search space of the learning model. This paper aims at capturing a snapshot of current trends in activity recognition with deep learning models. We have also examined the merits, demerits, efficiency of pioneering deep learning models being used for activity recognition.
All You Can Eat: High Performance Capacity and Plasticity in the Common Big-Eared Bat, Micronycteris microtis (Chiroptera: Phyllostomidae)

Ecological specialization and resource partitioning are expected to be particularly high in the species-rich communities of tropical vertebrates, yet many species have broader ecological niches than expected. In Neotropical ecosystems, Neotropical leaf-nosed bats (Phyllostomidae) are one of the most ecologically and functionally diverse vertebrate clades. Resource partitioning in phyllostomids might be achieved through differences in the ability to find and process food. We selected Micronycteris microtis, a very small (5–7 g) animalivorous phyllostomid, to explore whether broad resource use is associated with specific morphological, behavioral and performance traits within the phyllostomid radiation. We documented processing of natural prey and measured bite force in free-ranging M. microtis and other sympatric phyllostomids. We found that M. microtis had a remarkably broad diet for prey size and hardness. For the first time, we also report the consumption of vertebrates (lizards), which makes M. microtis the smallest carnivorous bat reported to date. Compared to other phyllostomids, M. microtis had the highest bite force for its size and cranial shape and high performance plasticity. Bite force and cranial shape appear to have evolved rapidly in the M. microtis lineage. High performance capacity and high efficiency in finding motionless prey might be key traits that allow M. microtis, and perhaps other species, to successfully co-exist with other gleaning bats.
Nonparametric Sparsification of Complex Multiscale Networks

Many real-world networks tend to be very dense. Particular examples of interest arise in the construction of networks that represent pairwise similarities between objects. In these cases, the networks under consideration are weighted, generally with positive weights between any two nodes. Visualization and analysis of such networks, especially when the number of nodes is large, can pose significant challenges which are often met by reducing the edge set. Any effective “sparsification” must retain and reflect the important structure in the network. A common method is to simply apply a hard threshold, keeping only those edges whose weight exceeds some predetermined value. A more principled approach is to extract the multiscale “backbone” of a network by retaining statistically significant edges through hypothesis testing on a specific null model, or by appropriately transforming the original weight matrix before applying some sort of threshold. Unfortunately, approaches such as these can fail to capture multiscale structure in which there can be small but locally statistically significant similarity between nodes. In this paper, we introduce a new method for backbone extraction that does not rely on any particular null model, but instead uses the empirical distribution of similarity weight to determine and then retain statistically significant edges. We show that our method adapts to the heterogeneity of local edge weight distributions in several paradigmatic real world networks, and in doing so retains their multiscale structure with relatively insignificant additional computational costs. We anticipate that this simple approach will be of great use in the analysis of massive, highly connected weighted networks.
Measuring Responsibility and Cooperation in Learning Teams in the University Setting: Validation of a Questionnaire

Cooperative learning are being used increasingly in the university classroom, in order to promote teamwork among students, improve performance and develop interpersonal competences. Responsibility and cooperation are two fundamental pillars of cooperative learning. Team members’ responsibility is a necessary condition for the team’s success in the assigned tasks. Students must be aware that they depend on each other and should make their maximum effort. On the other hand, in efficient groups, the members cooperate and pool their efforts to achieve the proposed goals. In this research, we propose to create a Questionnaire of Group Responsibility and Cooperation in Learning Teams (CRCG). Participants in this work were 375 students from the Faculty of Teacher Training of the University of Extremadura (Spain). The CRCG has very acceptable psychometric characteristics, good internal consistency, and temporal reliability. Moreover, structural equation analysis allowed us to verify that the latent variables in the two factors found are well defined and, therefore, their assessment is adequate. Besides, we found high significant correlations between the Learning Team Potency Questionnaire (CPEA) and the total score and the factors of the CRCG. This tool will evaluate cooperative skills and offer faculty information in order to prepare students for teamwork and conflict resolution.
A Shared Decision-Making Primary Care Intervention for Type 2 Diabetes

PURPOSE The purpose of this study is to test the feasibility of a brief shared decision-making (SDM) goal-setting intervention among individuals with type 2 diabetes. METHODS A convenience sample of 58 patients from the University Internal Medicine Resident Clinic was recruited to participate in the study. Outcomes were tested through a pilot test of the intervention and ongoing conversations with clinic nursing staff and physicians. Patient outcomes included preintervention and postintervention hemoglobin A1C (HbA1c), weight and blood pressure levels, preintervention and postintervention patient survey questionnaires, and documented diabetes goals. RESULTS Most providers indicated that the SDM intervention did not impose major demands. Patient-centered interviewing and an SDM approach to goal setting led to 75.9% of patients having at least 1 diabetes management goal documented in their medical record after intervention. HbA1c level, weight, and diabetes empowerment score showed a trend toward improvement, as did patient ratings of "life disruption from having diabetes. " Postintervention perceived knowledge of diabetes and treatments increased significantly (P = .001), as did the mean numbers of documented diabetes management goals (P < .001). CONCLUSIONS An SDM intervention for individuals with type 2 diabetes appears to be feasible and may improve major diabetes outcomes in primary care. SDM workbooks and activities can encourage patients to identify realistic diabetes goals with primary care providers. These results are encouraging. Future randomized trials with larger samples are warranted.
Long-Lasting Immune Responses 4 Years after GAD-Alum Treatment in Children with Type 1 Diabetes

A phase II clinical trial with glutamic acid decarboxylase (GAD) 65 formulated with aluminium hydroxide (GAD-alum) has shown efficacy in preserving residual insulin secretion in children and adolescents with recent-onset type 1 diabetes (T1D). We have performed a 4-year follow-up study of 59 of the original 70 patients to investigate long-term cellular and humoral immune responses after GAD-alum-treatment. Peripheral blood mononuclear cells (PBMC) were stimulated in vitro with GAD65. Frequencies of naïve, central and effector memory CD4+ and CD8+ T cells were measured, together with cytokine secretion, proliferation, gene expression and serum GAD65 autoantibody (GADA) levels. We here show that GAD-alum-treated patients display increased memory T-cell frequencies and prompt T-cell activation upon in vitro stimulation with GAD65, but not with control antigens, compared with placebo subjects. GAD65-induced T-cell activation was accompanied by secretion of T helper (Th) 1, Th2 and T regulatory cytokines and by induction of T-cell inhibitory pathways. Moreover, post-treatment serum GADA titres remained persistently increased in the GAD-alum arm, but did not inhibit GAD65 enzymatic activity. In conclusion, memory T- and B-cell responses persist 4 years after GAD-alum-treatment. In parallel to a GAD65-induced T-cell activation, our results show induction of T-cell inhibitory pathways important for regulating the GAD65 immunity.
Short and long distance marker detection technique in outdoor and indoor environments for embedded systems

During the last years, the market of embedded vision-based systems has been growing at an accelerated rate. Virtual and augmented reality has the potential to become one of the most innovative technologies for the next decade. One of the most important aspects of these technologies is related to the spatial location of objects or people in defined environments, for which there are several techniques. One of the most widely used is based on visual marker recognition. The main problems of these approaches are related to the accuracy, the changing environments, the processing time, the operating range/distance and the price. The popularization of these technologies produces a pull effect toward the companies developing the best technology at the lowest price. This paper proposes a marker design and an algorithm to detect the markers under different ambient conditions, with a long range to be executed on embedded systems with low computational requirements. The proposed method reduces the existing problems in the state-of-the-art related to the use of different environments and conditions such as different distances or different illumination. Moreover, the requisites of the method are minimal to reduce the cost of deployment.
Body weight and 25-hidroxyvitamin D follicular levels: a prospective study of women submitted to in vitro fertilization

Objective Vitamin D deficiency has been largely related to infertility in animals. However, data demonstrating a direct association between hypovitaminosis D and infertility in humans are still conflicting. Increased body weight and an elevated body mass index (BMI) are known for their association with infertility. Therefore, this study attempted to verify whether increases in body weight and the BMI were associated with lower 25-hidroxyvitamin D [25(OH)D3] levels in the follicular fluid (FF) of patients treated for infertility with intracytoplasmic sperm injections (ICSI). This study aimed to assess the FF levels of 25(OH)D3 in women submitted to ICSI and correlate these levels with the different body weight and BMI values observed in the enrolled cohort. Methods The FF aspirates of 199 patients submitted to ICSI were collected after oocyte aspiration to check whether FF 25(OH)D3 levels were associated with weight regardless of the etiology of infertility. Chemiluminescent assays were used to assess FF 25(OH)D3 levels. The etiology of infertility was defined based on patient clinical history and follow-up. Results The patients enrolled in the study were divided into three groups according to their FF 25(OH)D3 levels, as follows: a) deficient (n=71; <20 ng/ml); b) insufficient (n=64; 21< 25(OH) D3>29 ng/ml); and c) sufficient (n=56 >30ng/ml) levels. Patients with lower FF 25(OH)D3 levels had a greater mean weight (64.1kg) when compared to patients with higher 25(OH)D3 levels (60.7kg), p<0.01. No differences were observed in terms of age or etiology of infertility. Conclusion The body weight of the individuals with FF 25(OH)D3 deficiency measured in single follicles was significantly higher regardless of the etiology of infertility. Further epidemiologic and molecular studies are required to verify whether the amount of follicular 25(OH)D3 affects the outcome of IVF procedures.
CRISPR Provides Acquired Resistance Against Viruses in Prokaryotes

Clustered regularly interspaced short palindromic repeats (CRISPR) are a distinctive feature of the genomes of most Bacteria and Archaea and are thought to be involved in resistance to bacteriophages. We found that, after viral challenge, bacteria integrated new spacers derived from phage genomic sequences. Removal or addition of particular spacers modified the phage-resistance phenotype of the cell. Thus, CRISPR, together with associated cas genes, provided resistance against phages, and resistance specificity is determined by spacer-phage sequence similarity.
Social stress buffering by friends in childhood and adolescence: Effects on HPA and oxytocin activity

ABSTRACT Previous research has demonstrated that before puberty, parents are able to buffer, and often completely block, cortisol responses to social evaluative stressors (e.g., Trier Social Stress Test; TSST). However, after puberty, parents no longer provide a powerful buffer of the HPA axis from a social-evaluative stressor. The current study investigates whether friends can buffer the HPA axis in both children and adolescents compared to parents and whether similar stress-ameliorating patterns can also be observed in oxytocin activity. A total of 109 participants (54 children aged 9–10 and 55 adolescents aged 15–16; half of each sex) completed the TSST and were randomly assigned to prepare for their speech with their parent or friend for 5 minutes beforehand. Salivary cortisol and urinary oxytocin were measured before and after the TSST. For children, cortisol responses were comparable regardless of who helped the child prepare the speech. For adolescents, however, friends actually amplified the cortisol response compared to parents. In addition, adolescents produced less oxytocin than children, as did males compared to females. Notably, for boys, oxytocin levels decreased across the session if participants prepared with a friend rather than their parent. The mean change was in the same direction but not significant for girls. These results indicate that friends do not take over the social buffering role by age 15–16, which may inform interventions in at-risk children and adolescents.
Conditional Function of Autoaggregative Protein Cah and Common cah Mutations in Shiga Toxin-Producing Escherichia coli

ABSTRACT Cah is a calcium-binding autotransporter protein involved in autoaggregation and biofilm formation. Although cah is widespread in Shiga toxin-producing Escherichia coli (STEC), we detected mutations in cah at a frequency of 31.3% in this pathogen. In STEC O157:H7 supershedder strain SS17, a large deletion results in a smaller coding sequence, encoding a protein lacking the C-terminal 71 amino acids compared with Cah in STEC O157:H7 strain EDL933. We examined the function of Cah in biofilm formation and host colonization to better understand the selective pressures for cah mutations. EDL933-Cah played a conditional role in biofilm formation in vitro: it enhanced E. coli DH5α biofilm formation on glass surfaces under agitated culture conditions that prevented autoaggregation but inhibited biofilm formation under hydrostatic conditions that facilitated autoaggregation. This function appeared to be strain dependent since Cah-mediated biofilm formation was diminished when an EDL933 cah gene was expressed in SS17. Deletion of cah in EDL933 enhanced bacterial attachment to spinach leaves and altered the adherence pattern of EDL933 to bovine recto-anal junction squamous epithelial (RSE) cells. In contrast, in trans expression of EDL933 cah in SS17 increased its attachment to leaf surfaces, and in DH5α, it enhanced its adherence to RSE cells. Hence, the ecological function of Cah appears to be modulated by environmental conditions and other bacterial strain-specific properties. Considering the prevalence of cah in STEC and its role in attachment and biofilm formation, cah mutations might be selected in ecological niches in which inactivation of Cah would result in an increased fitness in STEC during colonization of plants or animal hosts. IMPORTANCE Shiga toxin-producing Escherichia coli (STEC) harbors genes encoding diverse adhesins, and many of these are known to play an important role in bacterial attachment and host colonization. We demonstrated here that the autotransporter protein Cah confers on E. coli DH5α cells a strong autoaggregative phenotype that is inversely correlated with its ability to form biofilms and plays a strain-specific role in plant and animal colonization by STEC. Although cah is widespread in the STEC population, we detected a mutation rate of 31.3% in cah, which is similar to that reported for rpoS and fimH. The formation of cell aggregates due to increased bacterium-to-bacterium interactions may be disadvantageous to bacterial populations under conditions that favor a planktonic state in STEC. Therefore, a loss-of-function mutation in cah is likely a selective trait in STEC when autoaggregative properties become detrimental to bacterial cells and may contribute to the adaptability of STEC to fluctuating environments.
Automatic Detection of Instability Architectural Smells

Code smells represent well known symptoms of problems at code level, and architectural smells can be seen as their counterpart at architecture level. If identified in a system, they are usually considered more critical than code smells, for their effect on maintainability issues. In this paper, we introduce a tool for the detection of architectural smells that could have an impact on the stability of a system. The detection techniques are based on the analysis of dependency graphs extracted from compiled Java projects and stored in a graph database. The results combine the information gathered from dependency and instability metrics to identify flaws hidden in the software architecture. We also propose some filters trying to avoid possible false positives.
Undecidability of Domino Games and Hhp-Bisimilarity1

History preserving bisimilarity (hp-bisimilarity) and hereditary history preserving bisimilarity (hhp-bisimilarity) are behavioural equivalences taking into account causal relationships between events of concurrent systems. Their prominent feature is that they are preserved under action re nement, an operation important for the top-down design of concurrent systems. It is shown that, in contrast to hp-bisimilarity, checking hhp-bisimilarity for nite labelled asynchronous transition systems is undecidable, by a reduction from the halting problem of 2-counter machines. To make the proof more transparent a novel intermediate problem of checking domino bisimilarity for origin constrained tiling systems is introduced and shown undecidable. It is also shown that the unlabelled domino bisimilarity problem is undecidable, which implies undecidability of hhp-bisimilarity for unlabelled nite asynchronous systems. Moreover, it is argued that the undecidability of hhp-bisimilarity holds for nite elementary net systems.
4-Phenylbutyrate suppresses the unfolded protein response without restoring protein folding in Saccharomyces cerevisiae

Accumulation of unfolded secretory proteins in the endoplasmic reticulum (ER), namely ER stress, is hazardous to eukaryotic cells and promotes the unfolded protein response (UPR). Ire1 is an ER-located transmembrane protein that senses ER stress and triggers the UPR. According to previous in vitro experiments, 4-phenylbutyrate (4-PBA) works as a chemical molecular chaperone. Since 4-PBA attenuates the UPR in mammalian tissue cultures, this chemical may have clinical potential for restoring ER-stressing conditions. In this study, we investigated 4-PBA's mode of action using the yeast Saccharomyces cerevisiae as a model organism. Although 4-PBA blocked a dithiothreitol (DTT)-induced UPR, it did not appear to restore impairment of ER protein folding that was caused by DTT. Moreover, even under non-stress conditions, 4-PBA attenuated UPR that was induced by an Ire1 mutant that exhibits a substantial activity without sensing ER accumulation of unfolded proteins. We also found that 4-PBA drastically promotes the degradation of Ire1. These observations indicate that at least in the case of yeast cells, 4-PBA suppresses the UPR not through restoration of the ER function to correctly fold proteins. Instead, the accelerated degradation of Ire1 possibly explains the reason why the UPR is attenuated by 4-PBA.