Miracle-dz/UniFAR-FTUs huggingface dataset:
Regulated internalization of caveolae

Caveolae are specialized invaginations of the plasma membrane which have been proposed to play a role in diverse cellular processes such as endocytosis and signal transduction. We have developed an assay to determine the fraction of internal versus plasma membrane caveolae. The GPI-anchored protein, alkaline phosphatase, was clustered in caveolae after antibody-induced crosslinking at low temperature and then, after various treatments, the relative amount of alkaline phosphatase on the cell surface was determined. Using this assay we were able to show a time- and temperature-dependent decrease in cell-surface alkaline phosphatase activity which was dependent on antibody-induced clustering. The decrease in cell surface alkaline phosphatase activity was greatly accelerated by the phosphatase inhibitor, okadaic acid, but not by a protein kinase C activator. Internalization of clustered alkaline phosphatase in the presence or absence of okadaic acid was blocked by cytochalasin D and by the kinase inhibitor staurosporine. Electron microscopy confirmed that okadaic acid induced removal of caveolae from the cell surface. In the presence of hypertonic medium this was followed by the redistribution of groups of caveolae to the center of the cell close to the microtubule-organizing center. This process was reversible, blocked by cytochalasin D, and the centralization of the caveolar clusters was shown to be dependent on an intact microtubule network. Although the exact mechanism of internalization remains unknown, the results show that caveolae are dynamic structures which can be internalized into the cell. This process may be regulated by kinase activity and require an intact actin network.
Less Waste on Waist Measurements: Determination of Optimal Waist Circumference Measurement Site to Predict Visceral Adipose Tissue in Postmenopausal Women with Obesity

With obesity being a leading cause of preventable death, it is vital to understand how best to identify individuals with greater risk of metabolic disease, especially those with high visceral adipose tissue (VAT). This study aimed to determine whether three commonly used waist circumference (WC) measurement sites could provide accurate estimations of VAT, as determined by magnetic resonance imaging (MRI), which is a gold standard for measuring VAT, in postmenopausal women with obesity. VAT volume was measured by MRI of the total abdomen in 97 women aged 57.7 ± 0.4 years (mean ± SEM), mean body mass index 34.5 ± 0.2 kg/m2. WC was measured at the midpoint between the lowest rib and the iliac crest (WCmid), the narrowest point of the torso (WCnarrow), and at the level of the umbilicus (WCumbilicus). WC differed significantly according to measurement site, with WCnarrow (102.1 ± 0.7 cm) < WCmid (108.3 ± 0.7 cm) < WCumbilicus (115.7 ± 0.8 cm) (p < 0.001). WCmid, WCnarrow and WCumbilicus were all significantly correlated with VAT, as measured by MRI (r = 0.581, 0.563 and 0.390, respectively; p < 0.001 for all), but the relationships between WCmid or WCnarrow and VAT determined by MRI were stronger than for WCumbilicus. Measurement of either WCmid or WCnarrow provides valid estimates of VAT in postmenopausal women with obesity, with WCnarrow being favoured in light of its greater ease and speed of measurement in this population.
Identification of candidate genes and long non-coding RNAs associated with the effect of ATP5J in colorectal cancer

The incidence and development of colorectal cancer (CRC) is a process with multiple gene interactions. We have previously demonstrated that ATP synthase-coupling factor 6, mitochondrial (ATP5J) is associated with CRC migration and 5-fluorouracil resistance; nevertheless, the exact molecular mechanism remains unclear. The following study uses microarray and bioinformatics methods to identify candidate genes and long non-coding RNAs (lncRNAs) in CRC cells (two pairs) with upregulated and downregulated ATP5J. Briefly, a total of 2,190 differentially expressed mRNAs (DEmRNAs) were sorted. Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) was performed for 4 DEmRNAs to validate the results of microarray analysis. Functional annotation and pathway enrichment were analyzed for DEmRNAs using the Database for Annotation, Visualization and Integrated Discovery. Significantly enriched pathways included the regulation of gene expression and cell growth. The protein-protein interaction network was constructed, and AKT serine/threonine kinase 2 (AKT2) was considered as one of the hub genes. For further analysis, 51 DEmRNAs and 30 DElncRNAs were selected that were positively or negatively associated with the expression of ATP5J in the two cell pairs. X-inactive specific transcript (XIST), premature ovarian failure 1B (POF1B) and calmin (CLMN) were identified in the DEmRNA-DElncRNA co-expression network. The expression of AKT2 and XIST in CRC cells was confirmed by RT-qPCR. To sum up, the candidate genes and lncRNAs, as well as potential signaling pathways, which were identified using integrated bioinformatics analysis, could improve the understanding of molecular events involved in the function of ATP5J in CRC.
Reﬁned Search Tree Technique for Dominating Set on Planar Graphs 1

We establish a reﬁned search tree technique for the parameterized Dominating Set problem on planar graphs. Here, we are given an undirected graph and we ask for a set of at most k vertices such that each other graph vertex has at least one neighbor in this set. We derive search-tree based ﬁxed-parameter solving algorithms with running times O (8 k n ) and O (8 k k + n 3 ), where n is the number of vertices in the graph. For our search tree, we ﬁrstly provide a set of reduction rules. Secondly, we prove an intricate branching theorem based on the Euler formula. In addition, we give a family of example graphs showing that the bound of the branching theorem is optimal with respect to our reduction rules. Our ﬁnal search tree is very easy (to implement); its correctness analysis, however, is involved.
How Do Residents Spend Their Time in the Intensive Care Unit?

Purpose:To describe the work of residents and the distribution of their time in 6 intensive care units (ICUs) of 2 medical centers (MCs). Methods:A total of 242 hours of observation to capture data on tasks performed by residents in 6 ICUs, including adult, pediatric, medical and surgical units, were conducted. For each observation period, the percentages of total time spent on each task and on the aggregated task categories were calculated. Results:Overall, while in the ICUs, residents spent almost half of their time in clinical review and documentation (19%), conversation with team physicians (16%), conversation attendance (6%) and order management (6%). The 2 MCs differed in the time that residents spent on administrative review and documentation (4% in one MC and 15% in the other). The pediatric ICUs were similar in the 2 MCs, whereas the adult ICUs exhibited differences in the time spent on order management and administrative review and documentation. Conclusions:While in the ICUs, residents spent most time performing direct patient care and care coordination activities. The distribution of activities varied across 2 MCs and across ICUs, which highlights the need to consider the local context on residents' work in ICUs.
The First Metriorhynchid Crocodylomorph from the Middle Jurassic of Spain, with Implications for Evolution of the Subclade Rhacheosaurini

Background Marine deposits from the Callovian of Europe have yielded numerous species of metriorhynchid crocodylomorphs. While common in English and French Formations, metriorhynchids are poorly known from the Iberian Peninsula. Twenty years ago an incomplete, but beautifully preserved, skull was discovered from the Middle Callovian of Spain. It is currently the oldest and best preserved metriorhynchid specimen from the Iberian Peninsula. Until now it has never been properly described and its taxonomic affinities remained obscure. Methodology/Principal Findings Here we present a comprehensive description for this specimen and in doing so we refer it to a new genus and species: Maledictosuchus riclaensis. This species is diagnosed by numerous autapomorphies, including: heterodont dentition; tightly interlocking occlusion; lachrymal anterior process excludes the jugal from the preorbital fenestra; orbits longer than supratemporal fenestrae; palatine has two non-midline and one midline anterior processes. Our phylogenetic analysis finds Maledictosuchus riclaensis to be the basal-most known member of Rhacheosaurini (the subclade of increasingly mesopelagic piscivores that includes Cricosaurus and Rhacheosaurus). Conclusions/Significance Our description of Maledictosuchus riclaensis shows that the craniodental morphologies that underpinned the success of Rhacheosaurini in the Late Jurassic and Early Cretaceous, as a result of increasing marine specialization to adaptations for feeding on fast small-bodied prey (i.e. divided and retracted external nares; reorientation of the lateral processes of the frontal; elongate, tubular rostrum; procumbent and non-carinated dentition; high overall tooth count; and dorsolaterally inclined paroccipital processes), first appeared during the Middle Jurassic. Rhacheosaurins were curiously rare in the Middle Jurassic, as only one specimen of Maledictosuchus riclaensis is known (with no representatives discovered from the well-sampled Oxford Clay Formation of England). As such, the feeding/marine adaptations of Rhacheosaurini did not confer an immediate selective advantage upon the group, and it took until the Late Jurassic for this subclade to dominate in Western Europe.
Health-Promotion Practices of Young Black Women at Risk for Diabetes

PURPOSE The purpose of this study was to assess the health-promoting practices of young black women at risk for type 2 diabetes. METHODS The sample consisted of 30 black women from an urban area who had a history of gestational diabetes and/or a first-degree relative with diabetes. Participants completed the Health-Promoting Lifestyle Profile II Survey and an interview. Both were used to categorize health-promoting practices, exercise, diet, knowledge of diabetes prevention, and general health. RESULTS Demographic information and interview revealed a propensity towards obesity, despite education and income levels. The results for the Lifestyle II Survey showed a higher average total score for healthy nutrition than physical activity, which were inconsistent with the qualitative data obtained by interview. Fifty percent stated that they exercised as a general health-promoting behavior. Self-reported daily caloric, fiber, and fat intake was high to moderate; 60% reported initiating diet modifications secondary to a desire to lose weight or for medical problems; and 26% reported receiving information on diabetes prevention from a healthcare provider. CONCLUSIONS A systematic approach of planning and actively incorporating health-promoting activities into one's lifestyle as a young adult may protect or delay the onset of diabetes and prevent complications.
Cortical Representations of Speech in a Multitalker Auditory Scene

The ability to parse a complex auditory scene into perceptual objects is facilitated by a hierarchical auditory system. Successive stages in the hierarchy transform an auditory scene of multiple overlapping sources, from peripheral tonotopically based representations in the auditory nerve, into perceptually distinct auditory-object-based representations in the auditory cortex. Here, using magnetoencephalography recordings from men and women, we investigate how a complex acoustic scene consisting of multiple speech sources is represented in distinct hierarchical stages of the auditory cortex. Using systems-theoretic methods of stimulus reconstruction, we show that the primary-like areas in the auditory cortex contain dominantly spectrotemporal-based representations of the entire auditory scene. Here, both attended and ignored speech streams are represented with almost equal fidelity, and a global representation of the full auditory scene with all its streams is a better candidate neural representation than that of individual streams being represented separately. We also show that higher-order auditory cortical areas, by contrast, represent the attended stream separately and with significantly higher fidelity than unattended streams. Furthermore, the unattended background streams are more faithfully represented as a single unsegregated background object rather than as separated objects. Together, these findings demonstrate the progression of the representations and processing of a complex acoustic scene up through the hierarchy of the human auditory cortex. SIGNIFICANCE STATEMENT Using magnetoencephalography recordings from human listeners in a simulated cocktail party environment, we investigate how a complex acoustic scene consisting of multiple speech sources is represented in separate hierarchical stages of the auditory cortex. We show that the primary-like areas in the auditory cortex use a dominantly spectrotemporal-based representation of the entire auditory scene, with both attended and unattended speech streams represented with almost equal fidelity. We also show that higher-order auditory cortical areas, by contrast, represent an attended speech stream separately from, and with significantly higher fidelity than, unattended speech streams. Furthermore, the unattended background streams are represented as a single undivided background object rather than as distinct background objects.
Factors Influencing Abortion Decision-Making Processes among Young Women

Background: Decision-making about if and how to terminate a pregnancy is a dilemma for young women experiencing an unwanted pregnancy. Those women are subject to sociocultural and economic barriers that limit their autonomy and make them vulnerable to pressures that influence or force decisions about abortion. Objective: The objective of this study was to explore the individual, interpersonal and environmental factors behind the abortion decision-making process among young Mozambican women. Methods: A qualitative study was conducted in Maputo and Quelimane. Participants were identified during a cross-sectional survey with women in the reproductive age (15–49). In total, 14 women aged 15 to 24 who had had an abortion participated in in-depth interviews. A thematic analysis was used. Results: The study found determinants at different levels, including the low degree of autonomy for women, the limited availability of health facilities providing abortion services and a lack of patient-centeredness of health services. Conclusions: Based on the results of the study, the authors suggest strategies to increase knowledge of abortion rights and services and to improve the quality and accessibility of abortion services in Mozambique.
Potential diagnostic value of serum p53 antibody for detecting colorectal cancer: A meta-analysis

Numerous studies have assessed the diagnostic value of serum p53 (s-p53) antibody in patients with colorectal cancer (CRC); however, results remain controversial. The present study aimed to comprehensively and quantitatively summarize the potential diagnostic value of s-p53 antibody in CRC. The present study utilized databases, including PubMed and EmBase, systematically regarding s-p53 antibody diagnosis in CRC, accessed on and prior to 31 July 2016. The quality of all the included studies was assessed using quality assessment of studies of diagnostic accuracy (QUADAS). The result of pooled sensitivity, pooled specificity, positive likelihood ratio (PLR) and negative likelihood ratio (NLR) were analyzed and compared with overall accuracy measures using diagnostic odds ratios (DORs) and area under the curve (AUC) analysis. Publication bias and heterogeneity were also assessed. A total of 11 trials that enrolled a combined 3,392 participants were included in the meta-analysis. Approximately 72.73% (8/11) of the included studies were of high quality (QUADAS score >7), and all were retrospective case-control studies. The pooled sensitivity was 0.19 [95% confidence interval (CI), 0.18–0.21] and pooled specificity was 0.93 (95% CI, 0.92–0.94). Results also demonstrated a PLR of 4.56 (95% CI, 3.27–6.34), NLR of 0.78 (95% CI, 0.71–0.85) and DOR of 6.70 (95% CI, 4.59–9.76). The symmetrical summary receiver operating characteristic curve was 0.73. Furthermore, no evidence of publication bias or heterogeneity was observed in the meta-analysis. Meta-analysis data indicated that s-p53 antibody possesses potential diagnostic value for CRC. However, discrimination power was somewhat limited due to the low sensitivity.
Present and Future of Dengue Fever in Nepal: Mapping Climatic Suitability by Ecological Niche Model

Both the number of cases of dengue fever and the areas of outbreaks within Nepal have increased significantly in recent years. Further expansion and range shift is expected in the future due to global climate change and other associated factors. However, due to limited spatially-explicit research in Nepal, there is poor understanding about the present spatial distribution patterns of dengue risk areas and the potential range shift due to future climate change. In this context, it is crucial to assess and map dengue fever risk areas in Nepal. Here, we used reported dengue cases and a set of bioclimatic variables on the MaxEnt ecological niche modeling approach to model the climatic niche and map present and future (2050s and 2070s) climatically suitable areas under different representative concentration pathways (RCP2.6, RCP6.0 and RCP8.5). Simulation-based estimates suggest that climatically suitable areas for dengue fever are presently distributed throughout the lowland Tarai from east to west and in river valleys at lower elevations. Under the different climate change scenarios, these areas will be slightly shifted towards higher elevation with varied magnitude and spatial patterns. Population exposed to climatically suitable areas of dengue fever in Nepal is anticipated to further increase in both 2050s and 2070s on all the assumed emission scenarios. These findings could be instrumental to plan and execute the strategic interventions for controlling dengue fever in Nepal.
Climate change and groundwater: India’s opportunities for mitigation and adaptation

For millennia, India used surface storage and gravity flow to water crops. During the last 40 years, however, India has witnessed a decline in gravity-flow irrigation and the rise of a booming ‘water-scavenging’ irrigation economy through millions of small, private tubewells. For India, groundwater has become at once critical and threatened. Climate change will act as a force multiplier; it will enhance groundwater’s criticality for drought-proofing agriculture and simultaneously multiply the threat to the resource. Groundwater pumping with electricity and diesel also accounts for an estimated 16–25 million mt of carbon emissions, 4–6% of India’s total. From a climate change point of view, India’s groundwater hotspots are western and peninsular India. These are critical for climate change mitigation as well as adaptation. To achieve both, India needs to make a transition from surface storage to ‘managed aquifer storage’ as the center pin of its water strategy with proactive demand- and supply-side management components. In doing this, India needs to learn intelligently from the experience of countries like Australia and the United States that have long experience in managed aquifer recharge.
Proteomic Profiling Identifies Distinct Protein Patterns in Acute Myelogenous Leukemia CD34+CD38- Stem-Like Cells

Acute myeloid leukemia (AML) is believed to arise from leukemic stem-like cells (LSC) making understanding the biological differences between LSC and normal stem cells (HSC) or common myeloid progenitors (CMP) crucial to understanding AML biology. To determine if protein expression patterns were different in LSC compared to other AML and CD34+ populations, we measured the expression of 121 proteins by Reverse Phase Protein Arrays (RPPA) in 5 purified fractions from AML marrow and blood samples: Bulk (CD3/CD19 depleted), CD34-, CD34+(CMP), CD34+CD38+ and CD34+CD38-(LSC). LSC protein expression differed markedly from Bulk (n=31 cases, 93/121 proteins) and CD34+ cells (n= 30 cases, 88/121 proteins) with 54 proteins being significantly different (31 higher, 23 lower) in LSC than in either Bulk or CD34+ cells. Sixty-seven proteins differed significantly between CD34+ and Bulk blasts (n=69 cases). Protein expression patterns in LSC and CD34+ differed markedly from normal CD34+ cells. LSC were distinct from CD34+ and Bulk cells by principal component and by protein signaling network analysis which confirmed individual protein analysis. Potential targetable submodules in LSC included the proteins PU.1(SP1), P27, Mcl1, HIF1α, cMET, P53, Yap, and phospho-Stats 1, 5 and 6. Protein expression and activation in LSC differs markedly from other blast populations suggesting that studies of AML biology should be performed in LSC.
Fabrication of thick multilayered steel structure using A516 Grade 70 by multipass friction stir welding

In the present work, a thick-sectioned multilayered steel structure was fabricated by multipass friction stir welding on A516 Grade 70 steel. Tensile strength of the multilayered samples was comparable to that of the base metal. Failure was located in the base metal when a defect-free sample was tested. Charpy impact toughness was higher in the stir zone and heat affected zone than in the base metal. Higher microhardness values were found in the stir zone and heat affected zone than the base metal due to grain refinement and modification of the microstructures. Consequently, improved mechanical properties compared to the base metal were found in the weld zones of friction stir welded A516 Grade 70 steel.
Neuroinflammation in Autism: Plausible Role of Maternal Inflammation, Dietary Omega 3, and Microbiota

Several genetic causes of autism spectrum disorder (ASD) have been identified. However, more recent work has highlighted that certain environmental exposures early in life may also account for some cases of autism. Environmental insults during pregnancy, such as infection or malnutrition, seem to dramatically impact brain development. Maternal viral or bacterial infections have been characterized as disruptors of brain shaping, even if their underlying mechanisms are not yet fully understood. Poor nutritional diversity, as well as nutrient deficiency, is strongly associated with neurodevelopmental disorders in children. For instance, imbalanced levels of essential fatty acids, and especially polyunsaturated fatty acids (PUFAs), are observed in patients with ASD and other neurodevelopmental disorders (e.g., attention deficit hyperactivity disorder (ADHD) and schizophrenia). Interestingly, PUFAs, and specifically n-3 PUFAs, are powerful immunomodulators that exert anti-inflammatory properties. These prenatal dietary and immunologic factors not only impact the fetal brain, but also affect the microbiota. Recent work suggests that the microbiota could be the missing link between environmental insults in prenatal life and future neurodevelopmental disorders. As both nutrition and inflammation can massively affect the microbiota, we discuss here how understanding the crosstalk between these three actors could provide a promising framework to better elucidate ASD etiology.