Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of cytotoxicity features of antimicrobial peptides with potential to control bacterial diseases of citrus

Antimicrobial peptides (AMPs) can be found in various organisms, and could be considered an alternative for pesticides used to control plant pathogens, including those affecting citrus. Brazil is the largest producer and exporter of frozen concentrated orange juice in the world. However, the citrus industry has been affected by several diseases such as citrus canker and huanglongbing (HLB), caused by the bacteria Xanthomonas citri subsp. citri (X.citri) and Candidatus Liberibacter asiaticus (CaLas), respectively. In order to control these pathogens, putative AMPs were prospected in databases containing citrus sequences. Furthermore, AMPs already reported in the literature were also used for in vitro and in vivo assays against X.citri. Since CaLas cannot be cultivated in vitro, surrogates as Sinorhizobium meliloti and Agrobacterium tumefaciens were used. This study reports the evaluation of six AMPs obtained from different sources, two of them from Citrus spp. (citrus-amp1 and citrus-amp2), three from amphibians (Hylin-a1, K0-W6-Hy-a1 and Ocellatin 4-analogue) and one from porcine (Tritrpticin). Peptides K0-W6-Hy-a1, Ocellatin 4-analogue, and citrus-amp1 showed bactericidal activity against X.citri and S. meliloti and bacteriostatic effect on A. tumefaciens. These results were confirmed for X.citri in planta. In addition cytotoxicity evaluations of these molecules were performed. The AMPs that showed the lowest hemolytic activities were Triptrpticin, citrus-amp1 and citrus-amp2. Citrus-amp1 and citrus-amp2 not presented toxicity in experiments using in vivo model, G. mellonella and U87 MG cells. To verify the interaction of these AMPs with bacteria and erythrocyte cell membranes, vesicles mimicking these cells were built. Citrus-amp1 and Tritrpticin exhibited higher affinity to bacterial membranes, while Ocellatin 4-analogue and Hylin-a1 showed higher affinity to erythrocyte membranes; exclude their use in citrus. This work demonstrates an essential alternative, trough AMPs obtained from Citrus spp. , which can be feasibly used to control bacterial pathogens.
A Model to Predict 1‐Month Risk of Transplant or Death in Hepatitis A–Related Acute Liver Failure

Acute liver failure (ALF) caused by hepatitis A is a rare but fatal disease. Here, we developed a model to predict outcome in patients with ALF caused by hepatitis A. The derivation set consisted of 294 patients diagnosed with hepatitis A–related ALF (ALFA) from Korea, and a validation set of 56 patients from Japan, India, and United Kingdom. Using a multivariate proportional hazard model, a risk‐prediction model (ALFA score) consisting of age, international normalized ratio, bilirubin, ammonia, creatinine, and hemoglobin levels acquired on the day of ALF diagnosis was developed. The ALFA score showed the highest discrimination in the prediction of liver transplant or death at 1 month (c‐statistic, 0.87; 95% confidence interval [CI], 0.84‐0.92) versus King’s College criteria (KCC; c‐statistic, 0.56; 95% CI, 0.53‐0.59), U.S. Acute Liver Failure Study Group index specific for hepatitis A virus (HAV‐ALFSG; c‐statistic, 0.70; 95% CI, 0.65‐0.76), the new ALFSG index (c‐statistic, 0.79; 95% CI, 0.74‐0.84), Model for End‐Stage Liver Disease (MELD; c‐statistic, 0.79; 95% CI, 0.74‐0.84), and MELD including sodium (MELD‐Na; c‐statistic, 0.78; 95% CI, 0.73‐0.84) in the derivation set (all P < 0.01). In the validation set, the performance of the ALFA score (c‐statistic, 0.84; 95% CI, 0.74‐0.94) was significantly better than that of KCC (c‐statistic, 0.65; 95% CI, 0.52‐0.79), MELD (c‐statistic, 0.74; 95% CI, 0.61‐0.87), and MELD‐Na (c‐statistic, 0.72; 95% CI, 0.58‐0.85) (all P < 0.05), and better, but not statistically significant, than that of the HAV‐ALFSG (c‐statistic, 0.76; 95% CI, 0.61‐0.90; P = 0.28) and new ALFSG indices (c‐statistic, 0.79; 95% CI, 0.65‐0.93; P = 0.41). The model was well‐calibrated in both sets. Conclusion: Our disease‐specific score provides refined prediction of outcome in patients with ALF caused by hepatitis A.
Applications of sensory and physiological measurement in oral‐facial dental pain

Abstract Dentists regularly employ a variety of self‐report and sensory techniques to aid in the diagnosis and treatment of tooth‐related disease. Many of these techniques leverage principles borrowed from psychophysics, the quantitative measurement of the relationship between stimuli and evoked sensations, which falls under the larger umbrella of quantitative sensory testing (QST). However, most clinicians fail to meet the bar for what could be considered quantitative sensory testing, and instead focus on qualitative and dichotomous “yes/no” aspects of sensory experience. With our current subjective measurements for pain assessments, diagnosis and treatment of dental pain in young children and individuals (any age) with severe cognitive impairment rely extensively on third‐party observations. Consequently, the limitation of inadequate pain diagnosis can lead to poor pain management. In this review, it discusses mechanisms that underlie acute and chronic dental pain. It details the measurement of somatosensory responses and pulpal blood flow as objective measures of tooth health and pain. It proposes that bridging these varied methodologies will significantly improve diagnosis and treatment of orofacial pain and pathology. It concludes that improving the precision of sensory measurements could yield important improvements in diagnostic challenges in pulpal pathology for noncommunicative and cognitively impaired individuals.
Discovery of QTL Alleles for Grain Shape in the Japan-MAGIC Rice Population Using Haplotype Information

A majority of traits are determined by multiple quantitative trait loci (QTL) that can have pleiotropic effects. A multi-parent advanced generation inter-cross (MAGIC) population is well suited for genetically analyzing the effects of multiple QTL on traits of interest because it contains a higher number of QTL alleles than a biparental population. We previously produced the JAPAN-MAGIC (JAM) population, derived from eight rice (Oryza sativa L.) cultivars with high yield and biomass in Japan, and developed the method of genome-wide association study (GWAS) using haplotype information on the JAM lines. This method was effective for identifying major genes such as Waxy for eating quality and Sd1 for culm length. Here, we show that haplotype-based GWAS is also effective for the evaluation of multiple QTL with small effects on rice grain shape in the JAM lines. Although both the haplotype- and SNP-based GWAS identified multiple QTL for grain length and width, the sum of the estimated trait values of each allele for the QTL detected by haplotype-based GWAS had higher correlation with observed values than those detected by SNP-based GWAS, indicating high-accuracy QTL detection in the haplotype-based GWAS. Furthermore, the study revealed pleiotropic effects of some QTL regions in regulation of grain shape, suggesting that the haplotype-based GWAS using the JAM lines is an effective means to evaluate the main and side effects of haplotypes at each QTL. Information on the pleiotropic effects of haplotypes on various traits will be useful for designing ideal lines in a breeding program.
Ximmer: a system for improving accuracy and consistency of CNV calling from exome data

Detection of copy number variation (CNVs) is a challenging but highly valuable application of exome and targeted high throughput sequencing (HTS) data. While there are dozens of CNV detection methods available, using these methods remains challenging due to variable accuracy both across different data sets and within the same data set with different methods. We propose that extracting good results from CNV detection on HTS data requires a systematic approach involving rigorous quality control, adjustment of method parameters and calibration of confidence measures for filtering results. We present Ximmer, a tool which supports an end to end process for applying these procedures including a simulation framework, CNV detection analysis pipeline, and a visualisation and curation tool which enables interactive exploration of CNV results. We apply Ximmer to perform a comprehensive evaluation of CNV detection on four data sets using four different detection methods, representing one of the most comprehensive evaluations to date. Ximmer is open source and freely available at http://ximmer.org (example results are viewable at http://example.ximmer.org).
A genetic algorithm–based nonlinear scaling method for optimal motion cueing algorithm in driving simulator

A motion cueing algorithm plays an important role in generating motion cues in driving simulators. The motion cueing algorithm is used to transform the linear acceleration and angular velocity of a vehicle into the translational and rotational motions of a simulator within its physical limitation through washout filters. Indeed, scaling and limiting should be used along within the washout filter to decrease the amplitude of the translational and rotational motion signals uniformly across all frequencies through the motion cueing algorithm. This is to decrease the effects of the workspace limitations in the simulator motion reproduction and improve the realism of movement sensation. A nonlinear scaling method based on the genetic algorithm for the motion cueing algorithm is developed in this study. The aim is to accurately produce motions with a high degree of fidelity and use the platform more efficiently without violating its physical limitations. To successfully achieve this aim, a third-order polynomial scaling method based on the genetic algorithm is formulated, tuned, and implemented for the linear quadratic regulator–based optimal motion cueing algorithm. A number of factors, which include the sensation error between the real and simulator drivers, the simulator’s physical limitations, and the sensation signal shape-following criteria, are considered in optimizing the proposed nonlinear scaling method. The results show that the proposed method not only is able to overcome problems pertaining to selecting nonlinear scaling parameters based on trial-and-error and inefficient usage of the platform workspace, but also to reduce the sensation error between the simulator and real drivers, while satisfying the constraints imposed by the platform boundaries.
Community Resilience Learning Collaborative and Research Network (C-LEARN): Study Protocol with Participatory Planning for a Randomized, Comparative Effectiveness Trial

This manuscript presents the protocol and participatory planning process for implementing the Community Resilience Learning Collaborative and Research Network (C-LEARN) study. C-LEARN is designed to determine how to build a service program and individual client capacity to improve mental health-related quality of life among individuals at risk for depression, with exposure to social risk factors or concerns about environmental hazards in areas of Southern Louisiana at risk for events such as hurricanes and storms. The study uses a Community Partnered Participatory Research (CPPR) framework to incorporate community priorities into study design and implementation. The first phase of C-LEARN is assessment of community priorities, assets, and opportunities for building resilience through key informant interviews and community agency outreach. Findings from this phase will inform the implementation of a two-level (program-level and individual client level) randomized study in up to four South Louisiana communities. Within communities, health and social-community service programs will be randomized to Community Engagement and Planning (CEP) for multi-sector coalition support or Technical Assistance (TA) for individual program support to implement evidence-based and community-prioritized intervention toolkits, including an expanded version of depression collaborative care and resources (referrals, manuals) to address social risk factors such as financial or housing instability and for a community resilience approach to disaster preparedness and response. Within each arm, the study will randomize individual adult clients to one of two mobile applications that provide informational resources on services for depression, social risk factors, and disaster response or also provide psychoeducation on Cognitive Behavioral Therapy to enhance coping with stress and mood. Planned data collection includes baseline, six-month and brief monthly surveys for clients, and baseline and 12-month surveys for administrators and staff.
Proving Anonymity for BILMIX

A reductionist proof for sender anonymity of an asymmetric bilinear pairing based mixnet (BILMIX) is presented. We give an experiment-based definition for anonymity and show that BILMIX possesses anonymity in the semi-honest model against static adversaries assuming that the co-Bilinear Diffie-Hellman Problem, the Matching Find-Guess Problem and the Matching Diffie-Hellman Problem are hard. A new problem called Divisible Decisional Factorized Diffie-Hellman Problem (DDFDHP) is introduced and showed that finding connection between data stored by the Registration Authority and the receiver is at least as hard as breaking DDF-DHP, with the assumption that secret keys of the Registration Authority and the special bulletin board are kept secret.
Exploring the Effects of Imitating Hand Gestures and Head Nods on L1 and L2 Mandarin Tone Production.

Purpose This study investigated the impact of metaphoric actions-head nods and hand gestures-in producing Mandarin tones for first language (L1) and second language (L2) speakers. Method In 2 experiments, participants imitated videos of Mandarin tones produced under 3 conditions: (a) speech alone, (b) speech + head nods, and (c) speech + hand gestures. Fundamental frequency was recorded for both L1 (Experiment 1) and L2 (Experiment 2a) speakers, and the output of the L2 speakers was rated for tonal accuracy by 7 native Mandarin judges (Experiment 2b). Results Experiment 1 showed that 12 L1 speakers' fundamental frequency spectral data did not differ among the 3 conditions. In Experiment 2a, the conditions did not affect the production of 24 English speakers for the most part, but there was some evidence that hand gestures helped Tone 4. In Experiment 2b, native Mandarin judges found limited conditional differences in L2 productions, with Tone 3 showing a slight head nods benefit in a subset of "correct" L2 tokens. Conclusion Results suggest that metaphoric bodily actions do not influence the lowest levels of L1 speech production in a tonal language and may play a very modest role during preliminary L2 learning.
MiRNA-16 inhibited oral squamous carcinoma tumor growth in vitro and in vivo via suppressing Wnt/β-catenin signaling pathway

Background Oral carcinoma, one of the most commonly diagnosed cancers, has a poor prognosis and low survival rate with treatment. In recent years, some studies reported the upregulation of miRNA-16 (miR-16) in the oral carcinoma, whereas some other studies confirmed the downregulation of miR-16. In the current study, we aimed to investigate the function of miR-16 in oral carcinoma. Materials and methods Cell proliferation assay was measured by MTT assay, quantitative real time polymerase chain reaction (qRT-PCR) was used to evaluate the expression of miR-16, and apoptosis was analyzed by flow cytometry. In addition, the expression of proteins was detected by Western blot. Moreover, xenograft tumor model was established to detect the effect of miR-16 in vivo. Results The results suggested that miR-16 was downregulated in the oral carcinoma tissues. Overexpression of miR-16 inhibited the growth and proliferation of oral squamous carcinoma cells (OSCCs) and induced apoptosis both in vitro and in vivo, which is due to the suppression of Wnt/β-catenin signaling pathway. Conclusion This study provides evidence that overexpression of miR-16 inhibits OSCC growth by regulating Wnt/β-catenin signaling. Our findings suggest that overexpression of miR-16 could be a potential approach for gene therapy of OSCC in future.
Implicit Bias Predicts Liking of Ingroup Members Who Are Comfortable With Intergroup Interaction

We test a novel framework for how ingroup members are perceived during intergroup interaction. Across three experiments, we found that, above and beyond egalitarian attitudes and motivations, White observers’ automatic responses to Blacks (i.e., their implicit anti-Black bias) shaped their affiliation toward ingroup targets who appeared comfortable engaging in interracial versus same-race interaction. White observers’ implicit anti-Black bias negatively correlated with liking of White targets who were comfortable with Blacks (Experiments 1-3). The relationship between implicit bias and liking varied as a function of targets’ nonverbal comfort in interracial interactions (Experiment 1). Specifically, implicit bias negatively correlated with liking of targets when targets’ nonverbal behaviors revealed observers felt comfortable with interracial contact, irrespective of the nature of those behaviors (Experiment 2). Finally, the relationship between implicit bias and target liking was mediated by perceived similarity (Experiment 3). Theoretical implications for stigma-by-association, social network homogeneity, and extended contact are discussed.
Predictive Student Modeling for Interventions in Online Classes

As large-scale online classes become more prevalent there is great interest in finding ways to model students at scale in these classes in order to predict outcomes. Student models, if successful, would help determine strong predictors of student success, which would highlight potential causal factors for such success, allowing schools to focus on refinements and interventions that positively impact their student outcomes. In this research, TutorGen has partnered with Western Governors University (WGU), a large online university, and gathered data at scale in order to build exploratory models to predict student outcomes. This paper presents our results so far in successfully identifying students who will pass (or even take) the final exam. We have examined the order in which students take courses, as well as the timing of starting and completing work; our initial analysis reveals that these are strong predictors of course outcomes.
The importance of comorbidities in ischemic stroke: Impact of hypertension on the cerebral circulation

Comorbidities are a hallmark of stroke that both increase the incidence of stroke and worsen outcome. Hypertension is prevalent in the stroke population and the most important modifiable risk factor for stroke. Hypertensive disorders promote stroke through increased shear stress, endothelial dysfunction, and large artery stiffness that transmits pulsatile flow to the cerebral microcirculation. Hypertension also promotes cerebral small vessel disease through several mechanisms, including hypoperfusion, diminished autoregulatory capacity and localized increase in blood–brain barrier permeability. Preeclampsia, a hypertensive disorder of pregnancy, also increases the risk of stroke 4–5-fold compared to normal pregnancy that predisposes women to early-onset cognitive impairment. In this review, we highlight how comorbidities and concomitant disorders are not only risk factors for ischemic stroke, but alter the response to acute ischemia. We focus on hypertension as a comorbidity and its effects on the cerebral circulation that alters the pathophysiology of ischemic stroke and should be considered in guiding future therapeutic strategies.
The Effectiveness of Botulinum Toxin Type A Injections in the Management of Sialorrhea.

Objective The aim of this study was to evaluate the effect of Botulinum toxin type A by injecting in the submandibular and parotid glands on the frequency and severity of sialorrhea. Methods Pediatric patients who were referred to our department with sialorrhea were evaluated using their parents' frequency and severity scores of sialorrhea with visual analog scales before and after 3 months of botulinum toxin type A injections. Bilateral submandibular and parotid glands were injected with Botulinum toxin type A. Results Twenty-seven pediatric patients who were referred to our department with a complaint of sialorrhea were included in this study. Seventeen patients were female and 10 were male. Severe sialorrhea with cerebral palsy was present in all the patients. There were no complications after the procedure. Conclusion Botulinum toxin A injected in the major salivary glands in pediatric patients with neurological disorders is a safe and effective method.
Analyses with the Video Head Impulse Test During the Canalith Repositioning Maneuver in Patients with Isolated Posterior Semicircular Canal Benign Paroxysmal Positional Vertigo.

Objective To evaluate the posterior semicircular canal (PSCC) functions using video head impulse test (vHIT) during canalith repositioning maneuver (CRM) treatment in patients with isolated, posterior semicircular canal benign paroxysmal positional vertigo (PSCC-BPPV). Methods A total of 44 subjects comprising of 24 subjects with isolated PSCC-BPPV and 20 age- and sex-matched healthy control subjects were enrolled in the present study. vHIT was performed for the affected PSCC before and just after CRM and at the third and seventh day and first month to evaluate vestibulo-ocular reflex (VOR) gain, gain asymmetry (GA), and corrective saccades. Repeated determinations of VOR gain and GA were compared to evaluate the time course of vHIT measurements during CRM treatment in isolated PSCC-BPPV patients, and the values were also compared with the control group. Results VOR gains and GA values were not statistically different before and after CRM and at the third-day, seventh-day and first-month visits for the affected PSCC. Moreover, values did not differ between the BPPV and control groups, and none of the subjects demonstrated corrective saccades. Conclusion To our knowledge, this study is the first report to investigate vHIT measurements with a time course of alterations during CRM treatment in PSCC-BPPV patients. vHIT may not provide an additional contribution for evaluating vestibular dysfunction during the diagnosis and treatment of isolated PSCC-BPPV.
Ensuring and Restoring Balance on Access to Controlled Substances for Medical and Scientific Purposes: Joint Statement from Palliative Care Organizations

Abstract The central principle of “balance” represents the dual obligation of governments to establish a system of control that ensures the adequate availability of controlled substances for medical and scientific purposes while simultaneously preventing their nonmedical use, diversion, and trafficking, two primary goals of the international control system. On the one hand, although strong opioids, including morphine, are absolutely necessary for the relief of severe pain, legitimate access to opioids for pain treatment and palliative care is lacking in the majority of the world’s countries. On the other hand, in a few high-income countries with higher consumption of prescription opioids, diversion and nonmedical use are increasingly prevalent. This report presents examples of unbalanced systems and a joint statement from global and regional palliative care organizations to promote development of balanced systems for optimal public health outcomes. Although nonmedical use of controlled substances poses a risk to society, the system of control is not intended to be a barrier to their availability for medical and scientific purposes, nor to interfere in their legitimate medical use for patient care. As representatives of palliative care organizations, we urge heads of state to act and to take measures to ensure and restore balanced systems in their countries and call on public health leaders and regulators to work together.