Miracle-dz/UniFAR-FTUs huggingface dataset:
A new perspective: Establishing developmental profiles of premature infants based on Bayley-III scores at age 2

Abstract Longitudinal and cross-sectional studies in early childhood generally focus on different developmental areas separately. The aim of this study is to identify the most common developmental profiles regarding cognitive, language and motor skills among low birthweight (LBW) children. Our sample included 208 LBW children examined at 24–28 months. We used cluster analysis to identify developmental profiles based on the scores of the Bayley-III Cognitive, Language and Motor scales. We found three consistent profiles (High, Mildly Delayed and Severely Delayed) and three inconsistent, average profiles (with High Expressive Language, with Mildly Delayed Expressive Language and with Severely Delayed Language). Socioeconomic status, maternal education, in vitro fertilization, plurality and chronic morbidities were significantly related to the clusters. Cluster analysis might be an effective method to identify developmental profiles of preterm (and other at-risk) children, which might result in a more complex understanding of cognitive and psychomotor development in early childhood.
Accurate Global Potential Energy Surfaces for the H + CH3OH Reaction by Neural Network Fitting with Permutation Invariance.

The H + CH3OH reaction, which plays an important role in combustion and the interstellar medium, presents a prototypical system with multi channels and tight transition states. However, no globally reliable potential energy surface (PES) has been available to date. Here we develop global analytical PESs for this system using the permutation invariant polynomial-neural network (PIP-NN) and the high-dimensional neural network (HD-NN) methods based on a large number of data points calculated at the level of the explicitly correlated unrestricted coupled cluster single, double, and perturbative triple level with the augmented correlation corrected valence triple-zeta basis set (UCCSD(T)-F12a/AVTZ). We demonstrate that both machine learning PESs are able to accurately describe all dynamically relevant reaction channels. At a collision energy of 20 kcal/mol, quasi-classical trajectory calculations reveal that the dominant channel is the hydrogen abstraction from the methyl site, yielding H2 + CH2OH. The reaction of this major channel takes place mainly via the direct rebound mechanism. Both the vibrational and rotational states of the H2 product are relatively cold, and large portions of the available energy are converted into the product translational motion.
Why validation is not enough: Setting the scene for the implementation of the Kimberley Mum’s Mood Scale

Background The two part Kimberley Mum’s Mood Scale (KMMS) has been developed and validated as a culturally appropriate perinatal depression and anxiety screening tool for Aboriginal women living in the sparsely populated Kimberley region of North West Australia. As part of implementation aspects of user acceptability were explored to improve clinical utilisation of the KMMS. Methods Eighteen health professionals involved in perinatal care participated in an online survey or a qualitative semi-structured interview. Ten Aboriginal women (who held administrative, professional or executive roles) were subsequently interviewed in depth to further explore aspects of KMMS user acceptability. Results Many of the health professionals were not using the second part of the KMMS (the psychosocial discussion tool). Time constraints and a perception that the KMMS is only appropriate for women with literacy issues were identified by health professionals as significant barriers to KMMS uptake. In contrast the Aboriginal women interviewed considered the KMMS to be important for literate Aboriginal women and placed high value on having the time and space to ‘yarn’ with health professionals about issues that are important to them. Conclusion Implementing the KMMS across the Kimberley region requires health professionals to be trained. It also requires strategic engagement with health services to ensure health professionals and mangers understand the rationale and significance of the KMMS and are engaged in its successful implementation.
In silico subtractive genomics for target identification in human bacterial pathogens

Target identification is the first step in the drug and vaccine discovery process; in silico subtractive genomics is widely used in this process. Using this approach, in recent years, a large number of targets have been identified for bacterial pathogens that are either drug resistant or for which no suitable vaccine is available; most such reports concern a specific pathogen. The in silico method reduces the time as well as the cost of target screening. Although a powerful technique that can be applied to a wide range of pathogens, there are many pitfalls in the analysis and interpretation of the data. We review this approach, including targets that have been identified with this technique and various other aspects, including advantages and disadvantages. We also discuss our own experiences using this technology. Drug Dev Res 72: 162–177, 2011. © 2010 Wiley‐Liss, Inc.
Longer Hiding Time in Refuge Implies Greater Assessed Risk After Capture and Autotomy in Striped Plateau Lizards (Sceloporus virgatus)

Abstract During encounters with predators, prey that flee into refuges decide how long to hide. Refuge use theory predicts that hiding time increases as the risk of emerging increases. Lizards that escape by autotomizing their tails incur costs, including temporary decrease in speed and loss of ability to use autotomy. Thus, risk of being captured upon emergence is greater after autotomy. Also, a predator that captures a prey may later be assessed as posing greater threat. We predicted that hiding time increases after a lizard has been captured or has undergone autotomy. A previous study of striped plateau lizards (Sceloporus virgatus) showed that the proportion of lizards that entered refuges increased after autotomy but not after earlier capture. To examine unstudied effects of autotomy and capture on hiding time, we conducted a 2 × 2 factorial field experiment with handling and autotomy as factors. The four groups were (1) unhandled intact controls; (2) unhandled autotomized; (3) captured (and handled) intact, but not autotomized; and (4) captured, handled and autotomized. Because entering cool refuges entails costly decrease in body temperature, hiding times are shorter in cooler refuges. We controlled this effect statistically by conducting analyses of covariance incorporating difference in air temperature inside and outside refuges as the covariate. As predicted, autotomy and handling led to longer hiding times. However, handling affected hiding time only in intact lizards. Our results add autotomy and capture to risk factors known to affect hiding time, augmenting a growing body of knowledge supporting the hypothesis that trade-offs between costs of emerging and remaining in a refuge guide decisions about hiding time.
Computationally Efficient Cooperative Dynamic Range-Only SLAM Based on Sum of Gaussian Filter †

A cooperative dynamic range-only simultaneous localization and mapping (CDRO-SLAM) algorithm based on the sum of Gaussian (SoG) filter was recently introduced. The main characteristics of the CDRO-SLAM are (i) the integration of inter-node ranges as well as usual direct robot-node ranges to improve the convergence rate and localization accuracy and (ii) the tracking of any moving nodes under dynamic environments by resetting and updating the SoG variables. In this paper, an efficient implementation of the CDRO-SLAM (eCDRO-SLAM) is proposed to mitigate the high computational burden of the CDRO-SLAM due to the inter-node measurements. Furthermore, a thorough computational analysis is presented, which reveals that the computational efficiency of the eCDRO-SLAM is significantly improved over the CDRO-SLAM. The performance of the proposed eCDRO-SLAM is compared with those of several conventional RO-SLAM algorithms and the results show that the proposed efficient algorithm has a faster convergence rate and a similar map estimation error regardless of the map size. Accordingly, the proposed eCDRO-SLAM can be utilized in various RO-SLAM applications.
Molecular Simulations of PEGylated Biomolecules, Liposomes, and Nanoparticles for Drug Delivery Applications

Since the first polyethylene glycol (PEG)ylated protein was approved by the FDA in 1990, PEGylation has been successfully applied to develop drug delivery systems through experiments, but these experimental results are not always easy to interpret at the atomic level because of the limited resolution of experimental techniques. To determine the optimal size, structure, and density of PEG for drug delivery, the structure and dynamics of PEGylated drug carriers need to be understood close to the atomic scale, as can be done using molecular dynamics simulations, assuming that these simulations can be validated by successful comparisons to experiments. Starting with the development of all-atom and coarse-grained PEG models in 1990s, PEGylated drug carriers have been widely simulated. In particular, recent advances in computer performance and simulation methodologies have allowed for molecular simulations of large complexes of PEGylated drug carriers interacting with other molecules such as anticancer drugs, plasma proteins, membranes, and receptors, which makes it possible to interpret experimental observations at a nearly atomistic resolution, as well as help in the rational design of drug delivery systems for applications in nanomedicine. Here, simulation studies on the following PEGylated drug topics will be reviewed: proteins and peptides, liposomes, and nanoparticles such as dendrimers and carbon nanotubes.
Molecular mechanisms of splenectomy-induced hepatocyte proliferation

Functional and anatomical connection between the liver and the spleen is most clearly manifested in various pathological conditions of the liver (cirrhosis, hepatitis). The mechanisms of the interaction between the two organs are still poorly understood, as there have been practically no studies on the influence exerted by the spleen on the normal liver. Mature male Sprague-Dawley rats of 250–260 g body weight, 3 months old, were splenectomized. The highest numbers of Ki67+ hepatocytes in the liver of splenectomized rats were observed at 24 h after the surgery, simultaneously with the highest index of Ki67-positive hepatocytes. After surgical removal of the spleen, expression of certain genes in the liver tissues increased. A number of genes were upregulated in the liver at a single time point of 24 h, including Ccne1, Egf, Tnfa, Il6, Hgf, Met, Tgfb1r2 and Nos2. The expression of Ccnd1, Tgfb1, Tgfb1r1 and Il10 in the liver was upregulated over the course of 3 days after splenectomy. Monitoring of the liver macrophage populations in splenectomized animals revealed a statistically significant increase in the proportion of CD68-positive cells in the liver (as compared with sham-operated controls) detectable at 24 h and 48 h after the surgery. The difference in the liver content of CD68-positive cells between splenectomized and sham-operated animals evened out by day 3 after the surgery. No alterations in the liver content of CD163-positive cells were observed in the experiments. A decrease in the proportion of CD206-positive liver macrophages was observed at 48 h after splenectomy. The splenectomy-induced hepatocyte proliferation is described by us for the first time. Mechanistically, the effect is apparently induced by the removal of spleen as a major source of Tgfb1 (hepatocyte growth inhibitor) and subsequently supported by activation of proliferation factor-encoding genes in the liver.
Pharmacological ablation of the airway smooth muscle layer—Mathematical predictions of functional improvement in asthma

Airway smooth muscle (ASM) plays a major role in acute airway narrowing and reducing ASM thickness is expected to attenuate airway hyper‐responsiveness and disease burden. There are two therapeutic approaches to reduce ASM thickness: (a) a direct approach, targeting specific airways, best exemplified by bronchial thermoplasty (BT), which delivers radiofrequency energy to the airway via bronchoscope; and (b) a pharmacological approach, targeting airways more broadly. An example of the less well‐established pharmacological approach is the calcium‐channel blocker gallopamil which in a clinical trial effectively reduced ASM thickness; other agents may act similarly. In view of established anti‐proliferative properties of the macrolide antibiotic azithromycin, we examined its effects in naive mice and report a reduction in ASM thickness of 29% (p < .01). We further considered the potential functional implications of this finding, if it were to extend to humans, by way of a mathematical model of lung function in asthmatic patients which has previously been used to understand the mechanistic action of BT. Predictions show that pharmacological reduction of ASM in all airways of this magnitude would reduce ventilation heterogeneity in asthma, and produce a therapeutic benefit similar to BT. Moreover there are differences in the expected response depending on disease severity, with the pharmacological approach exceeding the benefits provided by BT in more severe disease. Findings provide further proof of concept that pharmacological targeting of ASM thickness will be beneficial and may be facilitated by azithromycin, revealing a new mode of action of an existing agent in respiratory medicine.
Inhibition of Human Low-Density Lipoprotein Oxidation in Relation to Composition of Phenolic Antioxidants in Grapes (Vitis vinifera)

Antioxidant activities of phenolic extracts from fourteen different types of fresh grapes were investigated by measuring the inhibition of human low-density lipoprotein (LDL) oxidation in vitro. The inhibition of LDL oxidation ranged from 22% to 60% at 10 μM gallic acid equivalents (GAE) of total phenols and from 62% to 91% at 20 μM GAE. The antioxidant activities were thus comparable to those previously found for wines. The relative LDL antioxidant activity correlated with the concentration of total phenols (r = 0.89, p < 0.01), with the level of anthocyanins (r = 0.56, p < 0.05) and flavonols (r = 0.54, p < 0.05) in the grape extracts as analyzed by high-performance liquid chromatography (HPLC). When seed crushing and longer extraction times were employed, high amounts of flavan-3-ols and hydroxybenzoates were extracted. With these extracts relative LDL antioxidant activity correlated highly with the levels of flavan-3-ols (r = 0.86, p < 0.01), total phenols (r = 0.79, p < 0.05), and hydroxybenzoates (r.
Resource and Pollen Limitations to Lifetime Seed Production in a Natural Plant Population

Using experimental manipulations, we examined pollen and resource limitations to seed production and their interaction in a natural population of a monocarpic plant, Ipomopsis aggregata. Our design cross two factors, pollen level (hand—pollinated or control) and resource level (water added, water and fertilizer added, or control). Both hand—pollination and fertilizing during the blooming season increased total seed production, while watering alone has no effect on any component of reproductive success. Hand—pollination boosted number of seeds per flower, with no effect on flower number. In contrasts, fertilizing had its primary effect on the number of flowers produced, while also increasing the number of seeds per mature fruit in hand—pollinated plants. Fertilizing increased nectar volume, but path analysis detected no indirect effect of this increased reward rate on seed production, suggesting instead that fertilizing has a slight, but direct, effect on seeds per flower. These results argue against a strict dichotomy between pollen limitation and resource limitation of female reproductive success in plants.
Source and Significance of Lysosomal Enzymes in Bovine Milk Fat Globule Membrane

Abstract Relationships of high somatic cell counts in milk to activity of enzymes phosphodiesterase, N-acetyl β -D-glucosaminidase, lipase, β -glucosidase alkaline phosphatase, and 5′-nucleotidase were investigated. Membrane yield and composition were determined also. Somatic cell counts in milk and washed cream were increased by intramammary infusions of bacterial endotoxin. The specific activity of all enzymes tended to increase when cell count increased. Leukocytic enzymes increased most. Heating had a similar effect on the rate of loss of lipase activity in somatic cells and in fat globule membranes. The amount of membrane recovered from quarters treated with endotoxin was slightly lower than that from control quarters, and it contained more neutral lipid, less phospholipid, and less protein than control samples. Some enzymes in fat globule membrane preparations may originate from milk leukocytes and should not be considered true enzymes of fat globule membrane. The presence of such enzymes in relation to changes in composition of fat globule membrane is discussed.
T cell receptor interactions with human leukocyte antigen govern indirect peptide selectivity for the cancer testis antigen MAGE-A4

T cell-mediated immunity is governed primarily by T cell receptor (TCR) recognition of peptide-human leukocyte antigen (pHLA) complexes and is essential for immunosurveillance and disease control. This interaction is generally stabilized by interactions between the HLA surface and TCR germline-encoded complementarity-determining region (CDR) loops 1 and 2, whereas peptide selectivity is guided by direct interactions with the TCR CDR3 loops. Here, we solved the structure of a newly identified TCR in complex with a clinically relevant peptide derived from the cancer testis antigen melanoma antigen-A4 (MAGE-A4). The TCR bound pHLA in a position shifted toward the peptide's N terminus. This enabled the TCR to achieve peptide selectivity via an indirect mechanism, whereby the TCR sensed the first residue of the peptide through HLA residue Trp-167, which acted as a tunable gateway. Amino acid substitutions at peptide position 1 predicted to alter the HLA Trp-167 side-chain conformation abrogated TCR binding, indicating that this indirect binding mechanism is essential for peptide recognition. These findings extend our understanding of the molecular rules that underpin antigen recognition by TCRs and have important implications for the development of TCR-based therapies.
Vision Based Wall Following Framework: A Case Study With HSR Robot for Cleaning Application

Periodic cleaning of all frequently touched social areas such as walls, doors, locks, handles, windows has become the first line of defense against all infectious diseases. Among those, cleaning of large wall areas manually is always tedious, time-consuming, and astounding task. Although numerous cleaning companies are interested in deploying robotic cleaning solutions, they are mostly not addressing wall cleaning. To this end, we are proposing a new vision-based wall following framework that acts as an add-on for any professional robotic platform to perform wall cleaning. The proposed framework uses Deep Learning (DL) framework to visually detect, classify, and segment the wall/floor surface and instructs the robot to wall follow to execute the cleaning task. Also, we summarized the system architecture of Toyota Human Support Robot (HSR), which has been used as our testing platform. We evaluated the performance of the proposed framework on HSR robot under various defined scenarios. Our experimental results indicate that the proposed framework could successfully classify and segment the wall/floor surface and also detect the obstacle on wall and floor with high detection accuracy and demonstrates a robust behavior of wall following.
Biomarkers and Strategy to Detect Preinvasive and Early Pancreatic Cancer: State of the Field and the Impact of the EDRN

Patients afflicted with pancreatic ductal adenocarcinoma (PDAC) face a dismal prognosis, but headway could be made if physicians could identify the disease earlier. A compelling strategy to broaden the use of surveillance for PDAC is to incorporate molecular biomarkers in combination with clinical analysis and imaging tools. This article summarizes the components involved in accomplishing biomarker validation and an analysis of the requirements of molecular biomarkers for disease surveillance. We highlight the significance of consortia for this research and highlight resources and infrastructure of the Early Detection Research Network (EDRN). The EDRN brings together the multifaceted expertise and resources needed for biomarker validation, such as study design, clinical care, biospecimen collection and handling, molecular technologies, and biostatistical analysis, and studies coming out of the EDRN have yielded biomarkers that are moving forward in validation. We close the article with an overview of the current investigational biomarkers, an analysis of their performance relative to the established benchmarks, and an outlook on the current needs in the field. The outlook for improving the early detection of PDAC looks promising, and the pace of further research should be quickened through the resources and expertise of the EDRN and other consortia. See all articles in this CEBP Focus section, “NCI Early Detection Research Network: Making Cancer Detection Possible. ”
A Prediction Tool for the Presence of Ceftriaxone-Resistant Uropathogens upon Hospital Admission

Antimicrobial resistance among uropathogens is a particularly pressing problem in the Asia-Pacific region. The objectives of this study were to determine the incidence and susceptibility of uropathogens upon hospital admission and to develop a risk-scoring model to predict the presence of ceftriaxone-resistance uropathogens (CrP). This was a retrospective observational cohort study of patients with a positive urine culture within 48 h of presentation at National University Hospital, Singapore between June 2015 and August 2015. Escherichia coli was the most common uropathogen isolated (51.7%), followed by Klebsiella pneumonia (15.1%) and Pseudomonas aeruginosa (8.2%). Overall, 372 out of 869 isolates (42.8%) were resistant to ceftriaxone. Hospitalization for ≥2 days within past 30 days, antibiotic use within the past 3 months and male gender were associated with the presence of CrP. A risk score based on these parameters successfully predicted CrP with an area under the curve of 0.68. The risk score will help clinicians to accurately predict antibiotic resistance at the individual patient level and allow physicians to safely prescribe empiric ceftriaxone in patients at low risk of CrP, thus reducing the antibiotic selection pressure that is driving carbapenem resistance in hospitals throughout Asia.
Pathogenic SREK1 decrease in Huntington’s disease lowers TAF1 mimicking X-linked dystonia parkinsonism

A TAF1 mutation that lowers levels of the transcript causes X-linked dystonia parkinsonism. Hernández et al. show reduced levels of TAF1, and of the RNA-binding protein SREK1 which targets TAF1, also in Huntington’s disease. SREK1 overexpression restores TAF1 levels in the R6/1 mouse model, and reduces motor deficits.