Miracle-dz/UniFAR-FTUs huggingface dataset:
Safety, equity and monitoring: a review of the gaps in maternal vaccination strategies for Aboriginal and Torres Strait Islander women

ABSTRACT Influenza and pertussis infections are disproportionately higher among Aboriginal and Torres Strait Islander women and their infants compared to other Australians. These infections are potentially preventable through vaccination in pregnancy; however, there is a lack of systematic monitoring and therefore knowledge of vaccine uptake, safety and effectiveness in Australia, and specifically among Aboriginal and Torres Strait Islander women. The limited data available suggest there is a lower uptake of maternal vaccination among Aboriginal and Torres Strait Islander women compared to non-Aboriginal and Torres Strait Islander women, and this review seeks to explore potential reasons and the knowledge gaps in this regard. Other key gaps include the equitable access to quality antenatal care for Aboriginal and Torres Strait Islander women; and pregnancy loss <20 weeks gestation. Furthermore, our review highlights the importance of addressing these gaps in maternal vaccination strategies in partnership with Aboriginal and Torres Strait Islander peoples.
A High Protein Model Alters the Endometrial Transcriptome of Mares

High blood urea nitrogen (BUN) decreases fertility of several mammals; however, the mechanisms have not been investigated in mares. We developed an experimental model to elevate BUN, with urea and control treatments (7 mares/treatment), in a crossover design. Urea-treatment consisted of a loading dose of urea (0.03 g/kg of body weight (BW)) and urea injections over 6 h (0.03 g/kg of BW/h). Control mares received the same volume of saline solution. Blood samples were collected to measure BUN. Uterine and vaginal pH were evaluated after the last intravenous infusion, then endometrial biopsies were collected for RNA-sequencing with a HiSeq 4000. Cuffdiff (2.2.1) was used to identify the differentially expressed genes (DEG) between urea and control groups (false discovery rate-adjusted p-value < 0.1). There was a significant increase in BUN and a decrease of uterine pH in the urea group compared to the control group. A total of 193 genes were DEG between the urea and control groups, with five genes identified as upstream regulators (ETV4, EGF, EHF, IRS2, and SGK1). The DEG were predicted to be related to cell pH, ion homeostasis, changes in epithelial tissue, and solute carriers. Changes in gene expression reveal alterations in endometrial function that could be associated with adverse effects on fertility of mares.
Non-Invasive Tools to Detect Smoke Contamination in Grapevine Canopies, Berries and Wine: A Remote Sensing and Machine Learning Modeling Approach

Bushfires are becoming more frequent and intensive due to changing climate. Those that occur close to vineyards can cause smoke contamination of grapevines and grapes, which can affect wines, producing smoke-taint. At present, there are no available practical in-field tools available for detection of smoke contamination or taint in berries. This research proposes a non-invasive/in-field detection system for smoke contamination in grapevine canopies based on predictable changes in stomatal conductance patterns based on infrared thermal image analysis and machine learning modeling based on pattern recognition. A second model was also proposed to quantify levels of smoke-taint related compounds as targets in berries and wines using near-infrared spectroscopy (NIR) as inputs for machine learning fitting modeling. Results showed that the pattern recognition model to detect smoke contamination from canopies had 96% accuracy. The second model to predict smoke taint compounds in berries and wine fit the NIR data with a correlation coefficient (R) of 0.97 and with no indication of overfitting. These methods can offer grape growers quick, affordable, accurate, non-destructive in-field screening tools to assist in vineyard management practices to minimize smoke taint in wines with in-field applications using smartphones and unmanned aerial systems (UAS).
Randomized controlled trial of d-cycloserine in cocaine dependence: Effects on contingency management and cue-induced cocaine craving in a naturalistic setting.

Cocaine dependence constitutes a significant public health concern. This randomized, double-blind, placebo-controlled trial tested a novel approach to reducing cocaine use among cocaine-dependent individuals with d-cycloserine, a drug known to enhance learning and some learning-based therapies. Urine samples and cocaine craving were assessed across three phases: induction (Weeks 1-2), treatment (Weeks 3-5; urinalysis-based contingency management plus exposure therapy), and posttreatment (Weeks 6-7). During the treatment phase, either 50 mg of d-cycloserine or placebo was administered after delivery of urinalysis feedback with potential monetary reward and before exposure therapy sessions in naturalistic contexts individually associated with cocaine use. d-cycloserine significantly improved learning on an operant laboratory task. Contingency management significantly reduced cocaine use and craving. d-cycloserine did not significantly affect cocaine use or craving in the treatment phase. Craving significantly increased for the d-cycloserine group during the post treatment phase. Therefore, although the study showed that d-cycloserine was capable of improving learning, enhancement of learning-based therapy was not observed. Moreover, no differences in behavioral measures of cocaine demand (cocaine purchasing task) or monetary or sexual delay discounting were observed across phases or between groups in any phase. These results are somewhat consistent with previous findings suggesting that d-cycloserine administration increases cocaine craving, although they differ from other findings showing that d-cycloserine administration reduces alcohol or nicotine cravings. Methodological variables (e.g., guided vs. unguided exposure therapy sessions, length of extinction exposure) likely play a role in dissimilar findings observed across studies. (PsycINFO Database Record (c) 2019 APA, all rights reserved).
Introduction to Measurement of Avidity of Anti-Coxiella burnetii IgG in Diagnosis of Q Fever

Due to the atypical serological profile of some patients with primary Q fever infection who do not develop IgM against Coxiella burnetii, we developed an avidity test to distinguish recent or past infections. We tested 39 serum samples by immunofluorescence with conventional assay and after urea treatment from 26 patients at different stages of the disease. ABSTRACT Due to the atypical serological profile of some patients with primary Q fever infection who do not develop IgM against Coxiella burnetii, we developed an avidity test to distinguish recent or past infections. We tested 39 serum samples by immunofluorescence with conventional assay and after urea treatment from 26 patients at different stages of the disease. We observed a strong avidity in the 15 serum samples from patients with infections of >6 months and a low avidity for sera from patients with recent infections. A complete denaturation of the antibody-antigen complex was observed for patients for whom the time since the beginning of infection was <1 month and a mean of 2.06 ± 0.54 lowered titers when the infection was less than 3 months old. That was statistically significant compared to sera from patients with infections of greater than 6 months (mean 0.20 ± 0.41) and with infections between 3 and 6 months (mean, 1.17 ± 0.41) (P = 0.0022 and P < 0.0001, respectively). These results were visualized by Western blotting. We concluded that high avidity (≤1 lowered titer) ruled out infection during the last 6 months and that complete denaturation was related to an infection which had occurred within the previous 3 months. Between these two situations, the avidity test is inconclusive. We suggest using an avidity test for atypical Q fever serology that could be misclassified as residual antibodies (IgG against C. burnetii detected without active or recent infection) and for pregnant women risking obstetrical complications. This new test will dramatically improve the diagnosis and management of patients with Q fever.
Metabolic constraints on synaptic learning and memory.

Dendritic spines, the carriers of long-term memory, occupy a small fraction of cortical space, and yet they are the major consumers of brain metabolic energy. What fraction of this energy goes for synaptic plasticity, correlated with learning and memory? It is estimated here based on neurophysiological and proteomic data for rat brain that, depending on the level of protein phosphorylation, the energy cost of synaptic plasticity constitutes a small fraction of the energy usedfor fast excitatory synaptic transmission, typically $4.0-11.2 \%$. Next, this study analyzes a metabolic cost of a new learning and its memory trace in relation to the cost of prior memories, using a class of cascade models of synaptic plasticity. It is argued that these models must contain bidirectional cyclic motifs, related to protein phosphorylation, to be compatible with basic thermodynamic principles. For most investigated parameters longer memories generally require proportionally more energy to store. The exception are the parameters controlling the speed of molecular transitions (e.g. ATP driven phosphorylation rate), for which memory lifetime per invested energy can increase progressively for longer memories.Furthermore, in general, a memory trace decouples dynamically from a corresponding synaptic metabolic rate such that the energy expanded on a new learning and its memory trace constitutes in most cases only a small fraction of the baseline energy associated with prior memories. Taken together, these empirical and theoretical results suggest a metabolic efficiency of synaptically stored information.
Natural Born Laser Dyes: Excited-State Intramolecular Proton Transfer (ESIPT) Emitters and Their Use in Random Lasing Studies

A series of five excited-state intramolecular proton transfer (ESIPT) emitters based on a 2-(2′-hydroxyphenyl) benzoxazole (HBO) scaffold, functionalized with a mono-or bis-(trialkylsilyl) acetylene extended spacer are presented. Investigation of their photophysical properties in solution and in the solid-state in different matrix, along with ab initio calculations gave useful insights into their optical behavior. Random lasing studies were conducted on a series of PMMA doped thin films, showing the presence of stimulated emission above the threshold of pumping energy density (ρth ≈ 0.5–2.6 mJ cm−2). In this work, the similarity of four level laser systems is discussed in light of the ESIPT photocycle.
Diagnostic performance of 18F‐fluorodeoxyglucose positron emission tomography in the evaluation of glioma

Identifying glioma grade through imaging allows clinicians to recommend and accurately direct treatment. We sought to quantify the utility of FDG‐PET/CT (18F‐fluorodeoxyglucose positron emission tomography/computed tomography), alone and in combination with MRI, in identifying high‐grade regions of glioma.
Impact of tumor microenvironment on the efficacy of epidermal growth factor receptor‐tyrosine kinase inhibitors in patients with EGFR‐mutant non‐small cell lung cancer

We retrospectively investigated the impact of the tumor microenvironment (TME) on the efficacy of epidermal growth factor receptor (EGFR)‐tyrosine kinase inhibitors (TKIs) as first‐line treatment in 70 patients with advanced EGFR‐mutant non‐small cell lung cancer and who were seen at Osaka City University Hospital (Osaka, Japan) between August 2013 and December 2017. Using immunohistochemical staining with 28‐8 and D7U8C Abs, the tumor proportion score was assessed for programmed cell death‐1 ligand‐1 (PD‐L1), as high (50% or more) or low (less than 50%), and ligand‐2 (PD‐L2) expression, respectively. The extent of CD8+ tumor‐infiltrating lymphocytes was evaluated on a scale of 0‐3, with 0‐1 as low and 2‐3 as high. The TME of the 52 evaluable pretreatment specimens was categorized into 4 subtypes, according to the respective PD‐L1 tumor proportion and CD8+ scores, as follows: (a) high/high (13.5%, n = 7); (b) low/low (42.3%, n = 22); (c) high/low (17.3%, n = 9); and (d) low/high (26.9%, n = 14). Expression of PD‐L2 was significantly the highest in type 1 (57.1% vs 4.5% vs 11.1% vs 7.1%, respectively; P = .0090). Response rate was significantly the lowest in type 1 (14.3% vs 81.8% vs 66.7% vs 78.6%, respectively; P = .0085). Progression‐free survival was the shortest in type 1 and the longest in type 4 (median, 2.4 vs 11.3 vs 8.4 vs 17.5 months, respectively; P = .00000077). The efficacy of EGFR‐TKIs differed according to the TME, and the phenotype with high PD‐L1 and CD8+ expression might be the subset that would poorly benefit from such treatment.
In Silico Modeling of Biofilm Formation by Nontypeable Haemophilus influenzae In Vivo

Multiple respiratory illnesses are associated with formation of biofilms within the human airway by NTHI. However, a substantial amount of our understanding of the mechanisms that underlie NTHI biofilm formation is obtained from in vitro studies. Our in silico model that describes biofilm formation by NTHI within the middle ears of Chinchilla lanigera will help isolate processes potentially responsible for the differences between the morphologies of biofilms formed in vivo versus those formed in vitro. Thus, the in silico model can be used to glean mechanisms that underlie biofilm formation in vivo and connect those mechanisms to those obtained from in vitro experiments. The in silico model developed here can be extended to investigate potential roles of specific host responses (e.g., mucociliary clearance) on NTHI biofilm formation in vivo. The developed computational tools can also be used to analyze and describe biofilm formation by other bacterial species in vivo. ABSTRACT Biofilms formed by nontypeable Haemophilus influenzae (NTHI) bacteria play an important role in multiple respiratory tract diseases. Visual inspection of the morphology of biofilms formed during chronic infections shows distinct differences from biofilms formed in vitro. To better understand these differences, we analyzed images of NTHI biofilms formed in the middle ears of Chinchilla lanigera and developed an in silico agent-based model of the formation of NTHI biofilms in vivo. We found that, as in vitro, NTHI bacteria are organized in self-similar patterns; however, the sizes of NTHI clusters in vivo are more than 10-fold smaller than their in vitro counterparts. The agent-based model reproduced these patterns and suggested that smaller clusters occur due to elimination of planktonic NTHI cells by the host responses. Estimation of model parameters by fitting simulation results to imaging data showed that the effects of several processes in the model change during the course of the infection. IMPORTANCE Multiple respiratory illnesses are associated with formation of biofilms within the human airway by NTHI. However, a substantial amount of our understanding of the mechanisms that underlie NTHI biofilm formation is obtained from in vitro studies. Our in silico model that describes biofilm formation by NTHI within the middle ears of Chinchilla lanigera will help isolate processes potentially responsible for the differences between the morphologies of biofilms formed in vivo versus those formed in vitro. Thus, the in silico model can be used to glean mechanisms that underlie biofilm formation in vivo and connect those mechanisms to those obtained from in vitro experiments. The in silico model developed here can be extended to investigate potential roles of specific host responses (e.g., mucociliary clearance) on NTHI biofilm formation in vivo. The developed computational tools can also be used to analyze and describe biofilm formation by other bacterial species in vivo.
Factors Associated with Sustained Exergaming: Longitudinal Investigation

Background Exergaming is technology-driven physical activity (PA) which, unlike traditional video game play, requires that participants be physically active to play the game. Exergaming may have potential to increase PA and decrease sedentary behavior in youth, but little is known about sustained exergaming. Objective The objectives of this study were to describe the frequency, correlates, and predictors of sustained exergaming. Methods Data were available in AdoQuest (2005-11), a longitudinal investigation of 1843 grade 5 students in Montréal, Canada. This analysis used data from grade 9 (2008-09) and 11 (2010-11). Participants at Time 1 (T1; mean age 14 years, SD 0.8 ) who reported past-week exergaming (n=186, 19.1% of AdoQuest sample) completed mailed self-report questionnaires at Time 2 (T2; mean age 16 years, SD 0.8). Independent sociodemographic, psychological, and behavioral correlates (from T2)/predictors (from T1 or earlier) were identified using multivariable logistic regression. Results Of 186 exergamers at T1, 81 (44%) reported exergaming at T2. Being female and having higher introjected regulation (ie, a type of PA motivation indicative of internalizing PA as a behavior) were independent correlates. None of the predictors investigated were associated with sustained exergaming. Conclusions Almost half of grade 9 exergamers sustained exergaming for 2 years. Exergaming may be a viable approach to help adolescents engage in and sustain PA during adolescence. Sex and PA motivation may be important in the sustainability of exergaming.
Sex Matters: A Multivariate Pattern Analysis of Sex- and Gender-Related Neuroanatomical Differences in Cis- and Transgender Individuals Using Structural Magnetic Resonance Imaging

Abstract Univariate analyses of structural neuroimaging data have produced heterogeneous results regarding anatomical sex- and gender-related differences. The current study aimed at delineating and cross-validating brain volumetric surrogates of sex and gender by comparing the structural magnetic resonance imaging data of cis- and transgender subjects using multivariate pattern analysis. Gray matter (GM) tissue maps of 29 transgender men, 23 transgender women, 35 cisgender women, and 34 cisgender men were created using voxel-based morphometry and analyzed using support vector classification. Generalizability of the models was estimated using repeated nested cross-validation. For external validation, significant models were applied to hormone-treated transgender subjects (n = 32) and individuals diagnosed with depression (n = 27). Sex was identified with a balanced accuracy (BAC) of 82.6% (false discovery rate [pFDR] < 0.001) in cisgender, but only with 67.5% (pFDR = 0.04) in transgender participants indicating differences in the neuroanatomical patterns associated with sex in transgender despite the major effect of sex on GM volume irrespective of the self-identification as a woman or man. Gender identity and gender incongruence could not be reliably identified (all pFDR > 0.05). The neuroanatomical signature of sex in cisgender did not interact with depressive features (BAC = 74.7%) but was affected by hormone therapy when applied in transgender women (P < 0.001).
Artificial neural networks reveal individual differences in metacognitive monitoring of memory

Previous work supports an age-specific impairment for recognition memory of pairs of words and other stimuli. The present study tested the generalization of an associative deficit across word, name, and nonword stimulus types in younger and older adults. Participants completed associative and item memory tests in one of three stimulus conditions and made metacognitive ratings of perceptions of self-efficacy, task success (“postdictions”), strategy success, task effort, difficulty, fatigue, and stamina. Surprisingly, no support was found for an age-related associative deficit on any of the stimulus types. We analyzed our data further using a multilayer perceptron artificial neural network. The network was trained to classify individuals as younger or older and its hidden unit activities were examined to identify data patterns that distinguished younger from older participants. Analysis of hidden unit activities revealed that the network was able to correctly classify by identifying three different clusters of participants, with two qualitatively different groups of older individuals. One cluster of older individuals found the tasks to be relatively easy, they believed they had performed well, and their beliefs were accurate. The other cluster of older individuals found the tasks to be difficult, believed they were performing relatively poorly, yet their beliefs did not map accurately onto their performance. Crucially, data from the associative task were more useful for neural networks to discriminate between younger and older adults than data from the item task. This work underscores the importance of considering both individual and age differences as well as metacognitive responses in the context of associative memory paradigms.
Biophysical insights into the binding characteristics of bovine serum albumin with dipyridamole and the influence of molecular interaction with β cyclodextrin

Abstract The binding characteristic of anti-platelet drug dipyridamole has been investigated with a transport protein, serum albumin. A multi-spectroscopic approach has been employed, and the results were well supported by in silico molecular docking and simulation studies. The fluorescence quenching of serum albumin at three different temperatures revealed that the mechanism involved is static and the binding constant of the interaction was found to be of the order of 104 M−1. The reaction was found to be spontaneous and involved hydrophobic interactions. Synchronous, 3D fluorescence and CD spectroscopy indicated a change in conformation of bovine serum albumin (BSA) on interaction with DP. Using site-selective markers, the binding site of DP was found to be in subdomain IB. Molecular docking studies further corroborated these results. Molecular dynamic (MD) simulations showed lower RMSD values on interaction, suggesting the existence of a stable complex between DP and BSA. Furthermore, since β-Cyclodextrin (βCD) is used to improve the solubility of DP in ophthalmic solutions, therefore, the effect of (βCD) on the interaction of BSA and DP was also studied, and it was found that in the presence of βCD, the binding constant for BSA-DP interaction decreased. The present study is an attempt to characterize the transport of DP and to improve its bioavailability, consequently helping in dosage design to achieve optimum therapeutic levels. Communicated by Ramaswamy H. Sarma
Editorial Comment.

5. Gupta K, Hooton TM, Naber KG et al: International clinical practice guidelines for the treatment of acute uncomplicated cystitis and pyelonephritis in women: a 2010 update by the Infectious Diseases Society of America and the European Society for Microbiology and Infectious Diseases. Clin Infect Dis 2011; 52: e103. 6. Hooton TM and Gupta K: Acute simple cystitis in women. UpToDate. Available at https://www. uptodate.com/contents/acute-simple-cystitis-inwomen. Accessed January 31, 2019.