Miracle-dz/UniFAR-FTUs huggingface dataset:
Individuality and slow dynamics in bacterial growth homeostasis

Significance Microbial cells go through repeated cycles of growth and division. These cycles are not perfect: the time and size at division can fluctuate from one cycle to the next. Still, cell size is kept tightly controlled, and fluctuations do not accumulate to large deviations. How this control is implemented in single cells is still not fully understood. We performed experiments that follow individual bacteria in microfluidic traps for hundreds of generations. This enables us to identify distinct individual dynamic properties that are maintained over many cycles of growth and division. Surprisingly, we find that each cell suppresses fluctuations with a different strength; this variability defines an “individual” behavior for each cell, which is inherited along many generations. Microbial growth and division are fundamental processes relevant to many areas of life science. Of particular interest are homeostasis mechanisms, which buffer growth and division from accumulating fluctuations over multiple cycles. These mechanisms operate within single cells, possibly extending over several division cycles. However, all experimental studies to date have relied on measurements pooled from many distinct cells. Here, we disentangle long-term measured traces of individual cells from one another, revealing subtle differences between temporal and pooled statistics. By analyzing correlations along up to hundreds of generations, we find that the parameter describing effective cell size homeostasis strength varies significantly among cells. At the same time, we find an invariant cell size, which acts as an attractor to all individual traces, albeit with different effective attractive forces. Despite the common attractor, each cell maintains a distinct average size over its finite lifetime with suppressed temporal fluctuations around it, and equilibration to the global average size is surprisingly slow (>150 cell cycles). To show a possible source of variable homeostasis strength, we construct a mathematical model relying on intracellular interactions, which integrates measured properties of cell size with those of highly expressed proteins. Effective homeostasis strength is then influenced by interactions and by noise levels and generally varies among cells. A predictable and measurable consequence of variable homeostasis strength appears as distinct oscillatory patterns in cell size and protein content over many generations. We discuss implications of our results to understanding mechanisms controlling division in single cells and their characteristic timescales.
Genomic Regions Analysis of Seedling Root Traits and Their Regulation in Responses to Phosphorus Deficiency Tolerance in CSSL Population of Elite Super Hybrid Rice

Phosphorus (P) is the essential macro-element supporting rice productivity. Quantitative trait loci (QTL) underlying related traits at the seedling stage under two different phosphorus levels was investigated in rice using a population of 76 Chromosomal Sequence Substitution Lines (CSSLs) derived from a cross between the maintainer variety XieqingzaoB (P stress tolerant) and the restorer variety Zhonghui9308 (P stress sensitive); the parents of super hybrid rice Xieyou9308. A genetic linkage map with 120 DNA marker loci was constructed. At logarithmic odd (LOD) value of 2.0, a total of seven QTLs were detected for studied traits under two P levels and their relative ratio. The LOD values ranged from 2.00 to 3.32 and explaining 10.82% to 18.46% of phenotypic variation. Three QTLs were detected under low phosphorus (P−), one under normal (P+) and three under their relative ratio (P−/P+) on the rice chromosomes 3, 5, 6, 8 and 10. No significant QTLs were found for shoot dry weight (SDW) and total dry weight (TDW). The pleiotropic QTLs influencing root number (qRN5) and root dry weight (qRDW5) as novel QTLs under P− level were detected near marker RM3638 on chromosome 5, which considered to directly contributing to phosphorus deficiency tolerance in rice. These QTLs need further analysis, including the fine mapping and cloning, which may use in molecular marker assisted breeding.
Mycoplasma pneumoniae Among Children Hospitalized With Community-acquired Pneumonia

Background The epidemiology of Mycoplasma pneumoniae (Mp) among US children (<18 years) hospitalized with community-acquired pneumonia (CAP) is poorly understood. Methods In the Etiology of Pneumonia in the Community study, we prospectively enrolled 2254 children hospitalized with radiographically confirmed pneumonia from January 2010-June 2012 and tested nasopharyngeal/oropharyngeal swabs for Mp using real-time polymerase chain reaction (PCR). Clinical and epidemiological features of Mp PCR-positive and -negative children were compared using logistic regression. Macrolide susceptibility was assessed by genotyping isolates. Results One hundred and eighty two (8%) children were Mp PCR-positive (median age, 7 years); 12% required intensive care and 26% had pleural effusion. No in-hospital deaths occurred. Macrolide resistance was found in 4% (6/169) isolates. Of 178 (98%) Mp PCR-positive children tested for copathogens, 50 (28%) had ≥1 copathogen detected. Variables significantly associated with higher odds of Mp detection included age (10-17 years: adjusted odds ratio [aOR], 10.7 [95% confidence interval {CI}, 5.4-21.1] and 5-9 years: aOR, 6.4 [95% CI, 3.4-12.1] vs 2-4 years), outpatient antibiotics ≤5 days preadmission (aOR, 2.3 [95% CI, 1.5-3.5]), and copathogen detection (aOR, 2.1 [95% CI, 1.3-3.3]). Clinical characteristics were non-specific. Conclusions Usually considered as a mild respiratory infection, Mp was the most commonly detected bacteria among children aged ≥5 years hospitalized with CAP, one-quarter of whom had codetections. Although associated with clinically nonspecific symptoms, there was a need for intensive care in some cases. Mycoplasma pneumoniae should be included in the differential diagnosis for school-aged children hospitalized with CAP.
Late Holocene vegetation changes in relation with climate fluctuations and human activity in Languedoc (southern France)

Holocene climate fluctuations and human activity since the Neolithic have shaped present-day Mediter-ranean environments. Separating anthropogenic effects from climatic impacts to better understand Mediterranean pale-oenvironmental changes over the last millennia remains a challenging issue. High-resolution pollen analyses were un-dertaken on two cores from the Palavasian lagoon system (Herault, southern France). These records allow reconstruction of vegetation dynamics over the last 4500 years. Results are compared with climatic, historical and archeological archives. A long-term aridification trend is highlighted during the late Holocene, and three superimposed arid events are recorded at 4600–4300, 2800–2400 and 1300–1100 cal BP. These periods of high-frequency climate variability coincide in time with the rapid climatic events observed in the Atlantic Ocean (Bond et al., 2001). From the Bronze Age (4000 cal BP) to the end of the Iron Age (around 2000 cal BP), the spread of sclerophyllous taxa and loss of forest cover result from anthropogenic impact. Classical Antiquity is characterized by a major reforestation event related to the concentration of rural activity and populations in coastal plains leading to forest recovery in the mountains. A major regional deforestation occurred at the beginning of the High Middle Ages. Around 1000 cal BP, forest cover is minimal while the cover of olive, chestnut and walnut expands in relation to increasing human influence. The present-day vegetation dominated by Mediterranean shrubland and pines has been in existence since the beginning of the 20th century.
Bayesian Inference of Regular Expressions from Human-Generated Example Strings

In programming by example, users "write" programs by generating a small number of input-output examples and asking the computer to synthesize consistent programs. We consider a challenging problem in this domain: learning regular expressions (regexes) from positive and negative example strings. This problem is challenging, as (1) user-generated examples may not be informative enough to sufficiently constrain the hypothesis space, and (2) even if user-generated examples are in principle informative, there is still a massive search space to examine. We frame regex induction as the problem of inferring a probabilistic regular grammar and propose an efficient inference approach that uses a novel stochastic process recognition model. This model incrementally "grows" a grammar using positive examples as a scaffold. We show that this approach is competitive with human ability to learn regexes from examples.
Holocene Asian monsoon evolution revealed by a pollen record from an alpine lake on the southeastern margin of the Qinghai–Tibetan Plateau, China

Abstract. We present the results of pollen analyses from a 1105 cm long sediment core from Wuxu Lake in southwestern China, which depict the variations of the East Asian winter monsoon (EAWM) and the Indian summer monsoon (ISM) during the last 12.3 ka. During the period of 12.3 to 11.3 cal ka BP, the dominance of Betula forest and open alpine shrub and meadow around Wuxu Lake indicates a climate with relatively cold winters and dry summers, corresponding to the Younger Dryas event. Between 11.3 and 10.4 cal ka BP, further expansion of Betula forest and the retreat of alpine shrubs and meadows reflect a greater seasonality with cold winters and gradually increasing summer precipitation. From 10.4 to 4.9 cal ka BP, the dense forest understory, together with the gradual decrease in Betula forest and increase in Tsuga forest, suggest that the winters became warmer and summer precipitation was at a maximum, corresponding to the Holocene climatic optimum. Between 4.9 and 2.6 cal ka BP, Tsuga forest and alpine shrubs and meadows expanded significantly, reflecting relatively warm winters and decreased summer precipitation. Since 2.6 cal ka BP, reforestation around Wuxu Lake indicates a renewed humid period in the late Holocene; however, the vegetation in the catchment may also have been affected by grazing activity during this period. The results of our study are generally consistent with previous findings; however, the timing and duration of the Holocene climatic optimum from different records are inconsistent, reflecting real contrast in local rainfall response to the ISM. Overall, the EAWM is broadly in-phase with the ISM on the orbital timescale, and both monsoons exhibit a trend of decreasing strength from the early to late Holocene, reflecting the interplay of solar insolation receipt between the winter and summer seasons and El Nino–Southern Oscillation strength in the tropical Pacific.
Effect of Magnesium Loading Dose on Insulin Resistance in Patients With Stress-Induced Hyperglycemia: A Randomized Clinical Trial

Objectives: There is currently no evidence that whether magnesium supplementation would improve stress-induced hyperglycemia (SIH) in critically ill patients. In this study, effects of magnesium loading dose on insulin resistance (IR) indices were evaluated in critically ill patients without diabetes having SIH. Methods: Seventy critically ill patients with SIH were assigned to receive a loading dose of magnesium (7.5 g of magnesium sulfate in 500 mL normal saline as intravenous infusion over an 8-hour period) or placebo. Changes in baseline of serum and intracellular magnesium and serum adiponectin (AD) levels, homeostasis model assessment of IR (HOMA-IR), and HOMA-AD ratio were assessed in this study. Results: Serum and intracellular magnesium levels increased significantly in patients in the magnesium group (P < .001). At day 3, there were significant differences between the magnesium group and the placebo group in the mean changes from baseline in the HOMA (between-group difference: −0.11; 95% confidence interval [CI]: −0.19 to −0.01; P = .02), the AD (between-group difference: 0.94; 95% CI: 0.41-1.48; P = .04), and the HOMA-AD ratio (between-group difference: −0.03; 95% CI: −0.04 to −0.01; P < .001). Conclusion: In the present study, a single-loading dose of intravenous magnesium improved IR indices in critically ill patients with SIH.
Criteria for assessing the quality of mHealth apps: a systematic review

Objective Review the existing studies including an assessment tool/method to assess the quality of mHealth apps; extract their criteria; and provide a classification of the collected criteria. Methods In accordance with the PRISMA statement, a literature search was conducted in MEDLINE, EMBase, ISI and Scopus for English language citations published from January 1, 2008 to December 22, 2016 for studies including tools or methods for quality assessment of mHealth apps. Two researchers screened the titles and abstracts of all retrieved citations against the inclusion and exclusion criteria. The full text of relevant papers was then individually examined by the same researchers. A senior researcher resolved eventual disagreements and confirmed the relevance of all included papers. The authors, date of publication, subject fields of target mHealth apps, development method, and assessment criteria were extracted from each paper. The extracted assessment criteria were then reviewed, compared, and classified by an expert panel of two medical informatics specialists and two health information management specialists. Results Twenty-three papers were included in the review. Thirty-eight main classes of assessment criteria were identified. These were reorganized by expert panel into 7 main classes (Design, Information/Content, Usability, Functionality, Ethical Issues, Security and Privacy, and User-perceived value) with 37 sub-classes of criteria. Conclusions There is a wide heterogeneity in assessment criteria for mHealth apps. It is necessary to define the exact meanings and degree of distinctness of each criterion. This will help to improve the existing tools and may lead to achieve a better comprehensive mHealth app assessment tool.
Biomarkers for Homologous Recombination Deficiency in Cancer

Defective DNA repair is a common hallmark of cancer. Homologous recombination is a DNA repair pathway of clinical interest due to the sensitivity of homologous recombination-deficient cells to poly-ADP ribose polymerase (PARP) inhibitors. The measurement of homologous recombination deficiency (HRD) in cancer is therefore vital to the appropriate design of clinical trials incorporating PARP inhibitors. However, methods to identify HRD in tumors are varied and controversial. Understanding existing and new methods to measure HRD is important to their appropriate use in clinical trials and practice. The aim of this review is to summarize the biology and clinical validation of current methods to measure HRD, to aid decision-making for patient stratification and translational research in PARP inhibitor trials. We discuss the current clinical development of PARP inhibitors, along with established indicators for HRD such as germline BRCA1/2 mutation status and clinical response to platinum-based therapy. We then examine newer assays undergoing clinical validation, including 1) somatic mutations in homologous recombination genes, 2) "genomic scar" assays using array-based comparative genomic hybridization (aCGH), single nucleotide polymorphism (SNP) analysis or mutational signatures derived from next-generation sequencing, 3) transcriptional profiles of HRD, and 4) phenotypic or functional assays of protein expression and localization. We highlight the strengths and weaknesses of each of these assays, for consideration during the design of studies involving PARP inhibitors.
Machine Learning–Based Radiomics for Molecular Subtyping of Gliomas

Purpose: The new classification announced by the World Health Organization in 2016 recognized five molecular subtypes of diffuse gliomas based on isocitrate dehydrogenase (IDH) and 1p/19q genotypes in addition to histologic phenotypes. We aim to determine whether clinical MRI can stratify these molecular subtypes to benefit the diagnosis and monitoring of gliomas. Experimental Design: The data from 456 subjects with gliomas were obtained from The Cancer Imaging Archive. Overall, 214 subjects, including 106 cases of glioblastomas and 108 cases of lower grade gliomas with preoperative MRI, survival data, histology, IDH, and 1p/19q status were included. We proposed a three-level machine-learning model based on multimodal MR radiomics to classify glioma subtypes. An independent dataset with 70 glioma subjects was further collected to verify the model performance. Results: The IDH and 1p/19q status of gliomas can be classified by radiomics and machine-learning approaches, with areas under ROC curves between 0.922 and 0.975 and accuracies between 87.7% and 96.1% estimated on the training dataset. The test on the validation dataset showed a comparable model performance with that on the training dataset, suggesting the efficacy of the trained classifiers. The classification of 5 molecular subtypes solely based on the MR phenotypes achieved an 81.8% accuracy, and a higher accuracy of 89.2% could be achieved if the histology diagnosis is available. Conclusions: The MR radiomics-based method provides a reliable alternative to determine the histology and molecular subtypes of gliomas. Clin Cancer Res; 24(18); 4429–36. ©2018 AACR.
Novel Flux Linkage Estimation Algorithm for a Variable Flux PMSM

This paper presents a novel algorithm for online rotor flux linkage estimation for a variable flux interior permanent magnet synchronous machine drive system at different flux density levels. A modified adaptive nonlinear filter is used to instantaneously estimate the amplitude, phase angle, and frequency of the major back EMF harmonic components, from which the total air-gap flux linkage is estimated. The algorithm avoids the averaging method that depends only on the fundamental back EMF component in estimating the air-gap flux linkage. The <italic>d</italic>-axis inductance versus current measurement test is performed at variable magnetization states to account for the <italic>d </italic>-axis inductance variation when estimating the rotor flux linkage. Since the stator winding resistance is temperature dependent, a thermocouple is used to obtain the actual stator winding temperature for accurate stator winding resistance measurement. The core loss resistance has been neglected for simplicity. The method was experimentally evaluated for different magnetization states and showed a good performance in tracking the rotor flux linkage variations. The method was tested for field-oriented control (FOC) schemes (<inline-formula> <tex-math notation="LaTeX">${\boldsymbol{i}_{\boldsymbol{d}}} = 0$</tex-math></inline-formula>) and for FOC with the negative <inline-formula><tex-math notation="LaTeX">$d$</tex-math></inline-formula>-axis current operation as well.
Should all patients with adrenal insufficiency or a subgroup of patients with prediabetes be treated with dual‐release hydrocortisone?

Guarnotta et al. compare the effects of dual-release (DR) hydrocortisone 36 months' treatment in 13 patients with primary adrenal insufficiency and 36 with secondary adrenal insufficiency, compared to conventional glucocorticoid treatment. A retrospective evaluation was conducted on the effects of 36 months of DR hydrocortisone therapy on visceral adiposity, insulin secretion and insulin sensitivity. Forty-nine patients with adrenal insufficiency were recruited. This article is protected by copyright. All rights reserved.
Sleep quality as a mediator of problematic smartphone use and clinical health symptoms

Background and aims Although smartphone use brings many benefits for adolescents, it is also associated with many serious health problems. This study examined the relationship between problematic smartphone use (PSU) and clinical health symptoms (e.g., body dysfunction) and the mediating effects of sleep quality on this relationship in adolescents. Methods Participants in this cross-sectional survey were 686 middle- and high-school students (girls = 55.7%, Mage = 12.98 ± 1.38 years). Participants completed self-report measures of PSU, sleep quality, and physical symptoms. Correlation analyses and structural equation modeling between adolescents’ PSU and the variables of interest were conducted. Results This study indicated that there was a significant positive correlation between PSU and health symptoms. Furthermore, sleep quality mediated the relationship between PSU and health symptoms. Discussion and conclusions Findings suggest that to promote health and wellness in adolescents, individuals should be encouraged to place boundaries on smartphone use, especially at bedtime. Reducing adolescents’ exposure to smartphone use in this way may hold promise for improving the efficacy of PSU prevention efforts for adolescents.
Comparative Effects of Auditory Electromyographic Biofeedback for Participants Who Are Blind and Sighted

This study examined differences in auditory electromyographic biofeedback (AEB) effects between participants who were sighted and blind. Past research makes clear that AEB is effective for people who are blind, particularly because of their reported superiority in auditory processing, but no study has directly compared AEB efficacy between participants who are sighted and blind. A total of 11 participants who were sighted and 10 who were blind performed a motor task requiring 20 nonfatiguing muscle contractions at 20% maximal voluntary contraction (MVC) with or without AEB. AEB reduced the error (calculated as the absolute difference of two consecutive contractions) among both participant groups, and the error for the group without biofeedback was greater for the participants who were blind than that for the sighted participants (5.20% ± 2.05% MVC and 3.30% ± 1.26% MVC, respectively; p < .05). This finding was consistent with subjective rating data, also indicating a trend toward greater difficulty for participants who were blind when performing without biofeedback. Moreover, the AEB/no biofeedback condition showed fewer errors for the participants who were blind than for the participants who were sighted during the last part of the task (p = .036), indicating that participants who were blind were better at maintaining the AEB effect. These data suggest that the poor motor performance of participants who were blind was greatly improved with AEB, suggesting important applications of AEB for assistive technologies, adapted sports, and activities of daily living.