Miracle-dz/UniFAR-FTUs huggingface dataset:
Meta-Omics Reveals Genetic Flexibility of Diatom Nitrogen Transporters in Response to Environmental Changes

Abstract Diatoms (Bacillariophyta), one of the most abundant and diverse groups of marine phytoplankton, respond rapidly to the supply of new nutrients, often out-competing other phytoplankton. Herein, we integrated analyses of the evolution, distribution, and expression modulation of two gene families involved in diatom nitrogen uptake (DiAMT1 and DiNRT2), in order to infer the main drivers of divergence in a key functional trait of phytoplankton. Our results suggest that major steps in the evolution of the two gene families reflected key events triggering diatom radiation and diversification. Their expression is modulated in the contemporary ocean by seawater temperature, nitrate, and iron concentrations. Moreover, the differences in diversity and expression of these gene families throughout the water column hint at a possible link with bacterial activity. This study represents a proof-of-concept of how a holistic approach may shed light on the functional biology of organisms in their natural environment.
Genetic Testing for Breast Cancer Susceptibility Should Be Offered before Unilateral Abdominally Based Free Flap Breast Reconstruction.

BACKGROUND Pathogenic mutations have been identified in approximately 10 percent of patients who present with breast cancer. Notably, failure to identify deleterious genetic mutations has particular implications for patients undergoing abdominally based breast reconstruction, as the donor site can be used only once. The authors sought to determine: (1) how many patients underwent genetic testing before unilateral abdominally based free flap breast reconstruction; (2) how often deleterious mutations were detected after abdominally based free flap breast reconstruction; and (3) the cost-effectiveness of expanding genetic testing in this patient population. METHODS The authors retrospectively identified all patients who underwent unilateral abdominally based free flap breast reconstruction at Brigham and Women's Hospital/Dana-Farber Cancer Institute between 2007 and 2016. Chart review was performed to collect relevant demographic and clinical data. Relevant hospital financial data were obtained. RESULTS Of the 713 who underwent free flap breast reconstruction, 160 patients met inclusion criteria, and mean follow-up was 5.8 years. Three patients (1.9 percent of 160) underwent contralateral surgery after completing reconstruction, two of whom had BRCA2 and one with ATM mutation. One hundred eleven patients met National Comprehensive Cancer Network guidelines for genetic testing, but of those only 55.9 percent (62 patients) were tested. Financial data revealed that testing every patient in the cohort would result in a net savings of $262,000. CONCLUSIONS During a relatively short follow-up period, a small percentage of patients were diagnosed with pathogenic mutations and underwent contralateral mastectomy and reconstruction. However, because of the costliness of surgery and the decreased cost of genetic testing, it is cost-effective to test every patient before unilateral abdominally based free flap breast reconstruction.
Low mood and depressive symptoms during perimenopause – Should General Practitioners prescribe hormone replacement therapy or antidepressants as the first-line treatment?

Perimenopausal women have an increased risk of developing new onset and recurrent mental health conditions such as anxiety, low mood and depressive symptoms. General Practitioners frequently prescribe antidepressants as the first-line treatment for these symptoms, despite clear lack of evidence for their efficacy and their unfavourable side effect profile. This article, written by a General Practitioner, gives a practical overview of the mental health symptoms which women may report to their General Practitioners during the menopausal transition and discusses underlying causes, assessment, risk factors and treatment options based on current evidence.
A fault tolerance protocol for stateless parallel processing

Application fault tolerance is defined as a property that enables any high performance computing (HPC) application to continue operating in the event of single or multiple component failures in the HPC processing system. Note that a fault tolerant HPC system typically does not support application fault tolerance since it merely isolates the failed components without providing non-stopping services to the running applications. Exception handlers in languages such as C++, Java and C# are a form of fault-tolerance programming. Unfortunately, for HPC applications, these tools are insufficient to provide application fault tolerance. Stateless Parallel Processing (SPP) refers to a multi-processor architecture and a parallel programming paradigm that contain the minimal number of exposed application states. A dataflow machine is naturally SPP. A tuple-space based parallel processing system, such as Linda or Synergy, is also SPP. A SPP application contains two types of components: stateless workers and stateful masters. Unlike message-passing and shared memory parallel processing systems, a SPP system provides high performance and high availability at the same time via an enhanced inter-processor communication layer. This dissertation focuses on the development of a low overhead fault tolerance method for protecting both stateless and stateful components in a SPP application. For the stateless component, shadow tuple along with shadow state recovery is designed with very small overhead; while, for the stateful component, a system-level non-blocking coordinated checkpoint/restart mechanism with socket support is devised to achieve the goal. A prototype of the proposed fault tolerance protocol for SPP has been implemented for the purpose of performance research. Results of the experiments performed using this prototype show the proposed fault tolerance protocol not only has better performance and scalability than any blocking protocols, but also has a provably small overhead.
Measuring the safety of the Tor network

We need a better understanding of how much anonymity the Tor network provides against a partial network adversary who observes and/or operates some of the network. Specifically, we want to understand the chances that this class of adversary can observe a user’s traffic coming into the network and also the corresponding traffic exiting the network. Most of our graphs historically have looked at the total number of relays over time. But this simple scalar doesn’t take into account relay capacity, exit policies, geographic or network location, etc. One concrete problem from this bad metric is that when many new relays show up (e.g. due to a political event1), we really don’t have any insight about how the diversity of the new relays compares to the rest of the network. The simplistic metric also gets misused in academic research papers to produce misleading results like “I can sign up 2% of the Tor relays and capture 50% of the paths,” when what they mean is “I can provide half the capacity in the Tor network and capture half the paths. ” There are four parts to this research problem. First, we need a broad array of metrics that reflect various instances of our partial network adversary. Second, we need to understand for each metric how stable it is (sensitivity analysis) and what changes in the Tor network would efficiently improve (or harm) it. Third, we should make the calculations as realistic as possible based on actual Tor client behavior. Last, we need a better infrastructure for comparing the safety impact from alternate design scenarios, for example different path selection or route balancing algorithms. We’d love to work with you2 to help answer these questions.
Development of Technetium-99m-Labeled BODIPY-Based Probes Targeting Lipid Droplets Toward the Diagnosis of Hyperlipidemia-Related Diseases

Hyperlipidemia causes systemic lipid disorder, which leads to hepatic steatosis and atherosclerosis. Thus, it is necessary to detect these syndromes early and precisely to improve prognosis. In the affected regions, abnormal formation and growth of lipid droplets is observed; therefore, lipid droplets may be a suitable target for the diagnosis of hyperlipidemia-related syndromes. In this study, we designed and synthesized [99mTc]Tc-BOD and [99mTc]Tc-MBOD composed of one technetium-99m and two BODIPY scaffolds with hydroxamamide (Ham) or N-methylated hydroxamamide (MHam) in radiochemical yields of 54 and 35%, respectively, with a radiochemical purity of over 95%. [99mTc]Tc-BOD showed significantly higher accumulation levels in foam cells than in non-foam cells (foam cells: 213.8 ± 64.8, non-foam cell: 126.2 ± 26.9 %dose/mg protein, p < 0.05) 2 h after incubation. In contrast, [99mTc]Tc-MBOD showed similar accumulation levels in foam cells and non-foam cells (foam cells: 92.2 ± 23.3, non-foam cell: 83.8 ± 19.8 %dose/mg protein). In normal mice, [99mTc]Tc-BOD exhibited gradual blood clearance (0.5 h: 4.98 ± 0.35, 6 h: 1.94 ± 0.12 %ID/g) and relatively high accumulation in the liver 6 h after administration (15.22 ± 1.72 %ID/g). Therefore, [99mTc]Tc-BOD may have potential as an imaging probe for detecting lipid droplets in disease lesions of hyperlipidemia.
Unplanned Heavy Episodic and High-Intensity Drinking: Daily-Level Associations With Mood, Context, and Negative Consequences.

OBJECTIVE Underestimating how much one will drink has been associated with greater alcohol-related consequences. Elevated mood or drinking context may relate to drinking more than planned (or intended) among college students. The aims of the current study were to test (a) whether positive and negative mood and contextual factors on a given day were associated with the likelihood of unplanned heavy drinking (defined as unplanned heavy episodic or high-intensity drinking), and (b) whether days with unplanned heavy drinking were associated with more negative consequences. METHOD The analytic sample included 352 college students (53.4% female; 71.3% non-Hispanic White) who completed daily assessments via automated telephone interviews. Multilevel models were used to test predictors of unplanned heavy drinking (Aim 1) and predictors of consequences (Aim 2). RESULTS Almost a third (29.60%) of drinking days were unplanned heavy drinking days. Individuals with higher average positive mood across the sampled days had lower odds of unplanned heavy drinking. No significant associations were observed between negative mood and unplanned heavy drinking. Weekend days and days with special occasions were associated with lower odds of unplanned heavy drinking. Unplanned heavy drinking was associated with more negative consequences on that day. CONCLUSIONS Students were frequently not able to accurately predict the amount of alcohol they would consume on that day, which conferred an increased risk of negative consequences. Interventions could incorporate strategies that help students anticipate their alcohol consumption in order to employ protective behavioral strategies in high-risk contexts.
Differential impairment of positive and negative schizotypy in list-method and item-method directed forgetting.

Schizophrenia is characterized by cognitive impairment and this impairment is expected to occur, albeit to a lesser degree, in people putatively at risk for schizophrenia. Two experiments assessed the relationship between directed forgetting (DF) and schizotypy, which is a multidimensional construct that reflects the expression of the underlying vulnerability for schizophrenia. Experiment 1 involved item-method DF and Experiment 2 involves list-method DF study. The schizotypy dimensions exhibited differential patterns of impairment across the 2 methods that suggest different underlying processes. Positive schizotypy showed impairment in item-method DF that was driven by reduced ability to forget forget-cued items, whereas performance on remember-cued items was unaffected in positive schizotypy. Despite the deficit in item-method DF, positive schizotypy participants showed preserved performance in list-method DF. The opposite pattern was found in negative schizotypy participants, who showed impairment in list-method DF, despite preserved performance in item-method DF. Negative schizotypy was previously associated with deficits in context processing and, consistent with context-change account of list-method DF, showed deficits in list-method DF task. Positive schizotypy is characterized by deficits in inhibitory control and, consistent with inhibitory account of item-method DF, showed deficits in item-method DF task. Collectively, these results (a) suggest that different DF methods involve different underlying mechanisms, (b) support the context-account of list-method DF and an inhibitory account of item-method DF, and (c) support the multidimensional model of schizotypy by showing differential impairment in positive and negative schizotypy across the 2 DF tasks. (PsycINFO Database Record (c) 2019 APA, all rights reserved).
Relating irritability and suicidal ideation using mood and anxiety

Background Suicide is common in the context of depression and bipolar disorders, but there remains a lack of understanding as to how suicide ideation, a common symptom of mood disorders, progresses to suicidal behaviour. Irritability, a feature of some types of depression, is thought to contribute to the development of suicidal behaviour, but these associations are not well established. Objective To examine the relationship between irritability and suicide ideation according to the subtype of depression expressed in patients with mood disorder. Methods 75 patients with mood disorders seen at the CADE (Clinical Assessment Diagnostic Evaluation) Clinic underwent clinical assessment for suicidal ideation (Paykel Suicide Scale), symptom severity (Young Mania Rating Scale (YMRS), Hamilton Rating Scale for Depression (HAM-D) (anxious depression), Montgomery-Åsberg Depression Rating Scale (MADRS) (melancholic depression)) and irritability (item 5 of the YMRS). Findings Interestingly, irritability correlated with mania (r=0.734, p<0.001 (YMRS)) and depressive symptom scores (r=0.369, p<0.001 (MADRS); r=0.477, p<0.001 (HAM-D)), which in turn correlated with suicide ideation scores (r=0.364, p<0.01 (MADRS); r=0.275, p=0.017 (HAM-D)). However, despite this indirect association, there was no direct correlation between irritability and suicide ideation (r=0.050, p>0.05). Conclusions The nature of the relationship between irritability and suicidal ideation is determined by the emotional context within which irritability operates. Clinical implications Findings suggest that rather than examining irritability alone, consideration of the subtype of depression, especially that of anxious depression, should be paramount in assessing suicide risk.
Sociolinguistically Informed Natural Language Processing: Automating Irony Detection

Abstract : Irony detection is an important problem in computational sociolinguistic tasks, such as automatic community detection on the web. But the ironic/sincere distinction has proven to be a particularly difficult classification problem. Existing Machine Learning (ML) and Natural Language Processing (NLP) approaches, which tend to rely on simple statistical models built on top of word counts, are not very good at it. We hypothesize that this is because, in contrast to most text classification problems, word counts and syntactic features alone do not constitute an adequate representation for verbal irony detection. Indeed, sociolinguistic theories of verbal irony imply that a model of the speaker is a necessary condition for irony detection, at least in certain cases.
An update on the current management of adult obstructive sleep apnoea.

BACKGROUND Obstructive sleep apnoea (OSA) is common in adults. Various contributing factors to this condition have resulted in the development of a number of potential treatment modalities, some of which are in evolution. A multidisciplinary team involving the general practitioner is an important aspect in providing personalised care. OBJECTIVE The aim of this review is to provide a clinical update on the recent developments and future directions in adult OSA management. DISCUSSION In-lab polysomnography remains important in the diagnosis of OSA, although home sleep studies have good specificity and sensitivity in particular subgroups of patients. First-line therapy in adult OSA is continuous positive airway pressure, with mandibular advancement splints and surgical intervention considered second-line. Adjunctive therapies include weight loss, avoidance of supine sleep, management of nasal obstruction, alcohol intake limitation and exercise. Advancements in medications targeting multiple neurophysiological pathways, and surgical insertion of hypoglossal nerve stimulator devices represent possible future treatment pathways in Australia.
Bodily maps of emotions are culturally universal.

Emotions are often felt in the body, and interoceptive feedback is an important component of conscious emotional experiences. Here, we provide support for the cultural universality of bodily sensations associated with 13 emotions in a large international sample (3,954 individuals from 101 countries; age range = 18-90). Participants were presented with 2 silhouettes of bodies alongside emotional words and asked to color the bodily regions whose activity they felt increasing or decreasing while they experienced each given emotion. We tested the effects of various background factors (i.e., age, sex, education, body mass index, nationality, civilization, and language) on the bodily sensation maps. Bodily sensations associated with emotions were concordant across the tested cultures (rs > 0.82) and across the sexes (r > 0.80). Bodily sensations weakened during aging (M rs = 0.11 across emotions). We conclude that universality in experiencing emotions in the body is stronger than the differences due to culture or sex. (PsycINFO Database Record (c) 2019 APA, all rights reserved).
A human pathogenic bacterium Shigella proliferates in plants through adoption of type III effectors for shigellosis.

Shigella, which infects primates, can be transmitted via fresh vegetables; however, its molecular interactions with plants have not been elucidated. Here, we show that four Shigella strains, S. boydii, S. sonnei, S. flexneri 2a, and S. flexneri 5a, proliferate at different levels in Arabidopsis thaliana. Microscopic studies revealed that these bacteria were present inside leaves and damaged plant cells. Green fluorescent protein (GFP)-tagged S. boydii and S. flexneri 5a colonized leaves only, whereas S. flexneri 2a colonized both leaves and roots. Using Shigella mutants lacking type III secretion systems (T3SSs), we found that T3SSs that regulate the pathogenesis of shigellosis in humans also play a central role in bacterial proliferation in Arabidopsis. Strikingly, the immunosuppressive activity of two T3S effectors, OspF and OspG, was required for proliferation of Shigella in Arabidopsis. Of note, delivery of OspF or OspG effectors inside plant cells upon Shigella inoculation was confirmed using a split GFP system. These findings demonstrate that the human pathogen Shigella can proliferate in plants by adapting immunosuppressive machinery used in the original host human.
Imaging Heart Dynamics With Ultrafast Cascaded-Wave Ultrasound

The heart is an organ with highly dynamic complexity, including cyclic fast electrical activation, muscle kinematics, and blood dynamics. Although ultrafast cardiac imaging techniques based on pulsed-wave ultrasound (PUS) have rapidly emerged to permit mapping of heart dynamics, they suffer from limited sonographic signal-to-noise ratio (SNR) and penetration due to insufficient energy delivery and inevitable attenuation through the chest wall. We hereby propose ultrafast cascaded-wave ultrasound (uCUS) imaging to depict heart dynamics in higher SNR and larger penetration than conventional ultrafast PUS. To solve the known tradeoff between the length of transmitted ultrasound signals and spatial resolution while achieving ultrafast frame rates (>1000 Hz), we develop a cascaded synthetic aperture (CaSA) imaging method. In CaSA, an array probe is divided into subapertures; each subaperture transmits a train of diverging waves. These diverging waves are weighted in both the aperture (i.e., spatial) and range (i.e., temporal) directions with a coding matrix containing only +1 and −1 polarity coefficients. A corresponding spatiotemporal decoding matrix is designed to recover backscattered signals. The decoded signals are thereafter beamformed and coherently compounded to obtain one high-SNR beamformed image frame. For CaSA with <inline-formula> <tex-math notation="LaTeX">$M$ </tex-math></inline-formula> subapertures and <inline-formula> <tex-math notation="LaTeX">$N$ </tex-math></inline-formula> cascaded diverging waves, sonographic SNR is increased by <inline-formula> <tex-math notation="LaTeX">$10\times $ </tex-math></inline-formula> log<inline-formula> <tex-math notation="LaTeX">$_{10}\,\,(N \times M)$ </tex-math></inline-formula> (dB) compared with conventional synthetic aperture (SA) imaging. The proposed uCUS with CaSA was evaluated with conventional SA and Hadamard-encoded SA (H-SA) methods in a calibration phantom for B-mode image quality and an <inline-formula> <tex-math notation="LaTeX">$in\,\, vivo$ </tex-math></inline-formula> human heart in a transthoracic setting for the quality assessment of anatomical, myocardial motion, and chamber blood power Doppler images. Our results demonstrated that the proposed uCUS with CaSA (4 subapertures, 32 cascaded waves) improved SNR (+20.46 dB versus SA, +14.83 dB versus H-SA) and contrast ratio (+8.44 dB versus SA, +7.81 dB versus H-SA) with comparable spatial resolutions to and at the same frame rates as benchmarks.
Impact of a Trauma-Informed Intervention for Youth and Staff on Rates of Violence in Juvenile Detention Settings

The majority of youth in the juvenile justice system have experienced multiple traumatic events in their lives, including community violence, physical abuse, neglect, and traumatic loss. These high prevalence rates, coupled with the known negative consequences of trauma in childhood and adolescence, have led to a greater emphasis on implementing trauma-informed services and practices within juvenile justice settings. However, although many stakeholders and government entities have expressed support for creating more trauma-informed juvenile justice systems, there is still limited empirical knowledge about which interventions are most effective at improving outcomes, particularly at the organizational or facility level. In an effort to fill this gap, the current study evaluated the impact of a trauma-informed milieu intervention, including skills training for youth and training for staff, on rates of violence at two secure juvenile detention facilities (N = 14,856) located in a large Northeastern city. The analyses revealed that the intervention was significantly related to a reduction of violent incidents in Facility A, with no impact on incidents in Facility B. Follow-up analyses revealed that a larger proportion of eligible youth in Facility A completed the skills group program as compared with eligible youth in Facility B (16% vs. 9%). This finding has important implications for the implementation of trauma-informed interventions for youth in juvenile detention settings, as it suggests that to impact outcomes at the facility level, a minimum threshold of youth may need to be exposed to the intervention. In addition, reductions in violence at Facility A were only realized after both staff training and youth skills components were implemented, suggesting that both components are necessary to create change at the facility level. Future research is needed to further explore the impact of organizational and implementation-level factors on trauma-informed care outcomes in juvenile justice settings.