Miracle-dz/UniFAR-FTUs huggingface dataset:
Transcriptome Analysis of Escherichia coli during dGTP Starvation

ABSTRACT Our laboratory recently discovered that Escherichia coli cells starved for the DNA precursor dGTP are killed efficiently (dGTP starvation) in a manner similar to that described for thymineless death (TLD). Conditions for specific dGTP starvation can be achieved by depriving an E. coli optA1 gpt strain of the purine nucleotide precursor hypoxanthine (Hx). To gain insight into the mechanisms underlying dGTP starvation, we conducted genome-wide gene expression analyses of actively growing optA1 gpt cells subjected to hypoxanthine deprivation for increasing periods. The data show that upon Hx withdrawal, the optA1 gpt strain displays a diminished ability to derepress the de novo purine biosynthesis genes, likely due to internal guanine accumulation. The impairment in fully inducing the purR regulon may be a contributing factor to the lethality of dGTP starvation. At later time points, and coinciding with cell lethality, strong induction of the SOS response was observed, supporting the concept of replication stress as a final cause of death. No evidence was observed in the starved cells for the participation of other stress responses, including the rpoS-mediated global stress response, reinforcing the lack of feedback of replication stress to the global metabolism of the cell. The genome-wide expression data also provide direct evidence for increased genome complexity during dGTP starvation, as a markedly increased gradient was observed for expression of genes located near the replication origin relative to those located toward the replication terminus. IMPORTANCE Control of the supply of the building blocks (deoxynucleoside triphosphates [dNTPs]) for DNA replication is important for ensuring genome integrity and cell viability. When cells are starved specifically for one of the four dNTPs, dGTP, the process of DNA replication is disturbed in a manner that can lead to eventual death. In the present study, we investigated the transcriptional changes in the bacterium E. coli during dGTP starvation. The results show increasing DNA replication stress with an increased time of starvation, as evidenced by induction of the bacterial SOS system, as well as a notable lack of induction of other stress responses that could have saved the cells from cell death by slowing down cell growth.
Self-reported history of seizure and baseline neurocognitive test performance in student-athletes: an initial investigation

ABSTRACT Objectives: Baseline neurocognitive assessment data can be critical in return to play (RTP) decision-making following a sport-related concussion (SRC). The literature indicates that many modifying factors of SRC have been studied empirically; however, there has been little investigation into the effect of a self-reported history of seizure(s) on baseline neurocognitive test data. The objective of this investigation was to determine whether a self-reported history of seizure(s) is associated with differences in baseline Immediate Post-Concussion Assessment and Cognitive Testing (ImPACT) performance. Methods: A retrospective analysis of 18,245 adolescent and young adult athletes’ ImPACT scores was performed. After application of inclusion and exclusion criteria, 7,391 participants were dichotomized into groups based on the presence or absence of a self-reported history of seizure. Participants reporting a history of seizure (n = 60) were matched on multiple variables in a 1:3 ratio with controls (n = 180) without a history of self-reported seizure. Baseline ImPACT composite scores were then compared between groups using either a 2-tailed t-test or a Mann-Whitney U-Test. Results: A significant between-group difference was observed in ImPACT visual motor speed composite scores (35.28 vs. 37.64, p = 0.029, Hedge’s g = 0.327), with the group self-reporting a history of seizure performing at inferior average scores. No significant between-group differences were detected in verbal memory, visual memory, reaction time, impulse control, or total symptom scores. Conclusion: Athletes with a history of self-reported seizure scored significantly lower on ImPACT visual motor speed compared to matched controls. As a solitary finding with a small effect size, the clinical significance of this difference is unclear. Apart from the decrease in visual-motor speed, this preliminary analysis suggests that athletes with a history of seizure might not have significantly different neurocognitive baseline test scores when compared with matched controls. Further empirical investigation is warranted to determine if a history of seizure is a modifying factor for SRC.
How Multidimensional Health Locus of Control predicts utilization of emergency and inpatient hospital services

Health locus of control may be an important predictor of health care utilization. We analyzed associations between health locus of control and frequency of emergency department visits and hospital admissions, and investigated self-rated health as a potential mediator. Overall, 863 patients in an urban emergency department completed the Multidimensional Health Locus of Control instrument, and self-reported emergency department use and hospital admissions in the last year. We found small but significant associations between Multidimensional Health Locus of Control and utilization, all of which were mediated by self-rated health. We conclude that interventions to shift health locus of control may change patients’ perceptions of their own health, thereby impacting utilization.
Web Based Visualization for Sports Data Pattern

In this paper, we present a method that aims to help the user's understanding on the sports data patterns. The proposed method extracts the node and link information from the sports data feed files and visualizes them using the force-directed graph in 2D space. The node and link information consists of the keywords obtained from the sports data feed. Olympic data feed files collected from several events were visualized by using the proposed method, and the results show that the proposed method is useful for understanding the sports data patterns.
A DSC Approach to Robust Adaptive NN Tracking Control for Strict-Feedback Nonlinear Systems

A robust adaptive tracking control approach is presented for a class of strict-feedback single-input-single-output nonlinear systems. By employing radial-basis-function neural networks to account for system uncertainties, the proposed scheme is developed by combining ¿dynamic surface control¿ and ¿minimal learning parameter¿ techniques. The key features of the algorithm are that, first, the problem of ¿explosion of complexity¿ inherent in the conventional backstepping method is avoided, second, the number of parameters updated online for each subsystem is reduced to 2, and, third, the possible controller singularity problem in the approximation-based adaptive control schemes with feedback linearization technique is removed. These features result in a much simpler adaptive control algorithm, which is convenient to implement in applications. In addition, it is shown via input-to-state stability theory and small gain approach that all signals in the closed-loop system are semiglobal uniformly ultimately bounded. Finally, three simulation examples are used to demonstrate the effectiveness of the proposed scheme.
Epigenetic Modifications and Head and Neck Cancer: Implications for Tumor Progression and Resistance to Therapy

Head and neck squamous carcinoma (HNSCC) is the sixth most prevalent cancer and one of the most aggressive malignancies worldwide. Despite continuous efforts to identify molecular markers for early detection, and to develop efficient treatments, the overall survival and prognosis of HNSCC patients remain poor. Accumulated scientific evidences suggest that epigenetic alterations, including DNA methylation, histone covalent modifications, chromatin remodeling and non-coding RNAs, are frequently involved in oral carcinogenesis, tumor progression, and resistance to therapy. Epigenetic alterations occur in an unsystematic manner or as part of the aberrant transcriptional machinery, which promotes selective advantage to the tumor cells. Epigenetic modifications also contribute to cellular plasticity during tumor progression and to the formation of cancer stem cells (CSCs), a small subset of tumor cells with self-renewal ability. CSCs are involved in the development of intrinsic or acquired therapy resistance, and tumor recurrences or relapse. Therefore, the understanding and characterization of epigenetic modifications associated with head and neck carcinogenesis, and the prospective identification of epigenetic markers associated with CSCs, hold the promise for novel therapeutic strategies to fight tumors. In this review, we focus on the current knowledge on epigenetic modifications observed in HNSCC and emerging Epi-drugs capable of sensitizing HNSCC to therapy.
Immunotherapy of head and neck cancer: Emerging clinical trials from a National Cancer Institute Head and Neck Cancer Steering Committee Planning Meeting

Recent advances have permitted successful therapeutic targeting of the immune system in head and neck squamous cell carcinoma (HNSCC). These new immunotherapeutic targets and agents are being rapidly adopted by the oncologic community and hold considerable promise. The National Cancer Institute sponsored a Clinical Trials Planning Meeting to address the issue of how to further investigate the use of immunotherapy in patients with HNSCC. The goals of the meeting were to consider phase 2 or 3 trial designs primarily in 3 different patient populations: those with previously untreated, human papillomavirus‐initiated oropharyngeal cancers; those with previously untreated, human papillomavirus‐negative HNSCC; and those with recurrent/metastatic HNSCC. In addition, a separate committee was formed to develop integrative biomarkers for the clinical trials. The meeting started with an overview of key immune components and principles related to HNSCC, including immunosurveillance and immune escape. Four clinical trial concepts were developed at the meeting integrating different immunotherapies with existing standards of care. These designs were presented for implementation by the head and neck committees of the National Cancer Institute‐funded National Clinical Trials Network. This article summarizes the proceedings of this Clinical Trials Planning Meeting, the purpose of which was to facilitate the rigorous development and design of randomized phase 2 and 3 immunotherapeutic trials in patients with HNSCC. Although reviews usually are published immediately after the meeting is held, this report is unique because there are now tangible clinical trial designs that have been funded and put into practice and the studies are being activated to accrual. Cancer 2017;123:1259–1271. © 2016 American Cancer Society.
Barriers to Local Public Health Chronic Disease Surveillance Through Health Information Exchange: A Capacity Assessment of Health Departments in the Health Information Network of South Texas

Health information exchanges (HIEs) offer potential data sources for public health agencies to improve chronic disease surveillance; however, public health has not yet capitalized on these data. This study identified barriers that public health departments participating in the Health Information Network of South Texas face regarding HIE and community-level surveillance of chronic diseases. This study focused on 2 health departments participating in the Health Information Network of South Texas. We administered a survey to inventory the technology infrastructure of health departments and conducted semistructured interviews of the local, state, and national officials. We identified 3 barriers to using HIE for disease surveillance: insufficient skilled staff, variation in how laws are interpreted, and lack of a coordinated public health information technology strategy. We provide 4 recommendations for policy and practice: personnel capacity development, interorganizational informatics collaboration, interim approaches to clarifying the legality of bidirectional HIE until overarching legislation is enacted, and development of an enterprise architecture plan.
Dopamine D2 Receptors Modulate Pyramidal Neurons in Mouse Medial Prefrontal Cortex through a Stimulatory G-Protein Pathway

Dopaminergic modulation of prefrontal cortex (PFC) is thought to play key roles in many cognitive functions and to be disrupted in pathological conditions, such as schizophrenia. We have previously described a phenomenon whereby dopamine D2 receptor (D2R) activation elicits afterdepolarizations (ADPs) in subcortically projecting (SC) pyramidal neurons within L5 of the PFC. These D2R-induced ADPs only occur following synaptic input, which activates NMDARs, even when the delay between the synaptic input and ADPs is relatively long (e.g., several hundred milliseconds). Here, we use a combination of electrophysiological, optogenetic, pharmacological, transgenic, and chemogenetic approaches to elucidate cellular mechanisms underlying this phenomenon in male and female mice. We find that knocking out D2Rs eliminates the ADP in a cell-autonomous fashion, confirming that this ADP depends on D2Rs. Hyperpolarizing current injection, but not AMPA receptor blockade, prevents synaptic stimulation from facilitating D2R-induced ADPs, suggesting that this phenomenon depends on the recruitment of voltage-dependent currents (e.g., NMDAR-mediated Ca2+ influx) by synaptic input. Finally, the D2R-induced ADP is blocked by inhibitors of cAMP/PKA signaling, insensitive to pertussis toxin or β-arrestin knock-out, and mimicked by Gs-DREADD stimulation, suggesting that D2R activation elicits the ADP by stimulating cAMP/PKA signaling. These results show that this unusual physiological phenomenon, in which D2Rs enhance cellular excitability in a manner that depends on synaptic input, is mediated at the cellular level through the recruitment of signaling pathways associated with Gs, rather than the Gi/o-associated mechanisms that have classically been ascribed to D2Rs. SIGNIFICANCE STATEMENT Dopamine D2 receptors (D2Rs) in the prefrontal cortex (PFC) are thought to play important roles in behaviors, including working memory and cognitive flexibility. Variation in D2Rs has also been implicated in schizophrenia, Tourette syndrome, and bipolar disorder. Recently, we described a new mechanism through which D2R activation can enhance the excitability of pyramidal neurons in the PFC. Here, we explore the underlying cellular mechanisms. Surprisingly, although D2Rs are classically assumed to signal through Gi/o-coupled G-proteins and/or scaffolding proteins, such as β-arrestin, we find that the effects of D2Rs on prefrontal pyramidal neurons are actually mediated by pathways associated with Gs-mediated signaling. Furthermore, we show how, via this D2R-dependent phenomenon, synaptic input can enhance the excitability of prefrontal neurons over timescales on the order of seconds. These results elucidate cellular mechanisms underlying a novel signaling pathway downstream of D2Rs that may contribute to prefrontal function under normal and pathological conditions.
The Role of Race and Gender in Nutrition Habits and Self-Efficacy: Results from the Young Adult Weight Loss Study

Overweight and obesity are a massive public health problem and young adults are at high risk for gaining weight once they enter a college. This study sought to examine gender and race as they relate to nutrition habits and self-efficacy in a population of diverse young adults from the Young Adult Weight Loss Study. Participants (N = 62) were 29% males, 38.7% white, 33.8% Asian, and 12.9% African American. Males had lower self-efficacy for healthy eating (mean score = 92.5, SD = 17.1) compared to females (mean = 102.3, SD = 13.7, p = 0.02). Males had higher consumption of sodium compared to females (4308 versus 3239 milligrams/day, p = 0.01). There were no significant differences across racial subgroups in self-efficacy for healthy eating (p = 0.67) or self-efficacy for exercise (p = 0.61). Higher self-efficacy scores for healthy eating were significantly associated with less total sodium (r = −0.37, p = 0.007), greater fruit consumption, and less saturated fat. Our results indicate that weight loss interventions should be individualized and that there may be specific areas to target that are different for men and women. Additional larger studies should be conducted to confirm if racial differences exist across nutrition habits and self-efficacy and to confirm gender differences noted in this study.
Differentially private query learning: From data publishing to model publishing

As one of the most influential privacy definitions, differential privacy provides a rigorous and provable privacy guarantee for data publishing. However, the curator has to release a large number of queries in a batch or a synthetic dataset in the Big Data era. Two challenges need to be tackled: one is how to decrease the correlation between large sets of queries, while the other is how to predict on fresh queries. This paper transfers the data publishing problem to a machine learning problem, in which queries are considered as training samples and a prediction model will be released rather than query results or synthetic datasets. When the model is published, it can be used to answer current submitted queries and predict results for fresh queries from the public. Compared with the traditional method, the proposed prediction model enhances the accuracy of query results for non-interactive publishing. We prove that learning model can successfully retain the utility of published queries while preserving privacy.
Using large-scale web data to facilitate textual query based retrieval of consumer photos

The rapid popularization of digital cameras and mobile phone cameras has lead to an explosive growth of consumer photo collections. In this paper, we present a (quasi) real-time textual query based personal photo retrieval system by leveraging millions of web images and their associated rich textual descriptions (captions, categories, etc.). After a user provides a textual query (e.g., "pool"), our system exploits the inverted file method to automatically find the positive web images that are related to the textual query "pool" as well as the negative web images which are irrelevant to the textual query. Based on these automatically retrieved relevant and irrelevant web images, we employ two simple but effective classification methods, k Nearest Neighbor (kNN) and decision stumps, to rank personal consumer photos. To further improve the photo retrieval performance, we propose three new relevance feedback methods via cross-domain learning. These methods effectively utilize both the web images and the consumer images. In particular, our proposed cross-domain learning methods can learn robust classifiers with only a very limited amount of labeled consumer photos from the user by leveraging the pre-learned decision stumps at interactive response time. Extensive experiments on both consumer and professional stock photo datasets demonstrated the effectiveness and efficiency of our system, which is also inherently not limited by any predefined lexicon.
Thermal Transport in Three-Dimensional Nanoarchitected Materials

Materials that simultaneously possess ultralow thermal conductivity, high stiffness, and damage tolerance are highly desirable for engineering applications. However, this combination of properties has never been demonstrated in a single material because thermal and mechanical properties are coupled in most fully dense and porous solids. A new class of lattice materials with nanoscale features, called nanolattices, can fill this void in the material property space by virtue of their architecture and nanoscale dimensions. Extensive work on nanolattice mechanical properties report their excellent stiffness-to-density ratio and recoverability from large compressive strains. In contrast, the framework for studying their thermal properties has not been established. Our work develops the computational and experimental tools necessary to study heat conduction in nanoarchitected materials and applies those tools to prove the viability of octet-truss nanolattices as multifunctional thermal insulators. We implement significant improvements to a phonon Monte Carlo method to solve the Boltzmann transport equation (BTE) in highly complex geometries like the octet-truss. No prior works solve the BTE in a domain as intricate as a nanolattice, so we create a geometry representation scheme that can model any arbitrary 3-D body. Our enhanced variance-reduced Monte Carlo code incorporates this scheme, allowing us to predict the thermal conductivity of nanolattices and analyze the phonon transport behavior in them. Results suggest that hollow-beam silicon nanolattices indeed reach ultralow thermal conductivities. Based on Monte Carlo and finite element simulations, we develop a predictive thermal conductivity model that accounts for both diffusive and radiative phonon transport in nanolattices. We also devise custom modifications to the 3ω method to experimentally measure the thermal conductivity of additively manufactured nanolattices. Since the serial fabrication process of nanolattices makes it costly to cover large areas, we design a specialized 3ω sample that minimizes the required structure size while maintaining good experimental sensitivity. We derive a new thermal model to account for conductive losses through the heater line in our novel sample geometry. 3ω measurements and compression tests of hollow-beam alumina nanolattices show that they combine ultralow thermal conductivity with excellent mechanical stiffness and resilience, which proves that nanolattices occupy a previously unreachable region in material property space. Our work provides motivation to further investigate and improve the thermal properties of architected materials.
Corticospinal gating during action preparation and movement in the primate motor cortex

During everyday actions there is a need to be able to withhold movements until the most appropriate time. This motor inhibition is likely to rely on multiple cortical and subcortical areas, but the primary motor cortex (M1) is a critical component of this process. However, the mechanisms behind this inhibition are unclear, particularly the role of the corticospinal system, which is most often associated with driving muscles and movement. To address this, recordings were made from identified corticospinal (PTN, n = 94) and corticomotoneuronal (CM, n = 16) cells from M1 during an instructed delay reach-to-grasp task. The task involved the animals withholding action for ~2 s until a GO cue, after which they were allowed to reach and perform the task for a food reward. Analysis of the firing of cells in M1 during the delay period revealed that, as a population, non-CM PTNs showed significant suppression in their activity during the cue and instructed delay periods, while CM cells instead showed a facilitation during the preparatory delay. Analysis of cell activity during movement also revealed that a substantial minority of PTNs (27%) showed suppressed activity during movement, a response pattern more suited to cells involved in withholding rather than driving movement. These results demonstrate the potential contributions of the M1 corticospinal system to withholding of actions and highlight that suppression of activity in M1 during movement preparation is not evenly distributed across different neural populations. NEW & NOTEWORTHY Recordings were made from identified corticospinal (PTN) and corticomotoneuronal (CM) cells during an instructed delay task. Activity of PTNs as a population was suppressed during the delay, in contrast to CM cells, which were facilitated. A minority of PTNs showed a rate profile that might be expected from inhibitory cells and could suggest that they play an active role in action suppression, most likely through downstream inhibitory circuits.