Miracle-dz/UniFAR-FTUs huggingface dataset:
Interim outcomes of delamanid for the treatment of MDR- and XDR-TB in South Korea

Objectives Delamanid is a new anti-TB drug, but few data exist on its use outside clinical trials. The purpose of this study was to evaluate the efficacy as well as the safety and tolerability of a delamanid-containing regimen for 24 weeks in the treatment of MDR- and XDR-TB. Methods We performed a retrospective cohort study among patients with MDR/XDR-TB who were treated with a delamanid-containing regimen in seven hospitals in South Korea. Results A total of 32 patients with MDR-TB, of which 6 (18.8%) were XDR-TB, were included and all completed 24 weeks of delamanid treatment. Of 19 patients (59.4%) who had positive culture sputum at the initiation of delamanid treatment, the proportion of culture conversion at 8 weeks was 72.2% (13 of 18) in solid medium and 50.0% (7 of 14) in liquid medium. The proportion of culture conversion at 24 weeks was 94.4% (17 of 18) in solid medium and 92.9% (13 of 14) in liquid medium. The median time to culture conversion was 33 days (range = 5-81) using solid medium and 57 days (range = 8-96) using liquid medium. Of the 32 patients, there was no serious adverse event or death. Three patients developed a transient QTcF of > 500 ms. Conclusions The use of delamanid combined with optimized background regimens has the potential to achieve high culture conversion rates at 24 weeks with an acceptable safety and tolerability profile in patients with MDR/XDR-TB.
Invariant recognition drives neural representations of action sequences

Recognizing the actions of others from visual stimuli is a crucial aspect of human perception that allows individuals to respond to social cues. Humans are able to discriminate between similar actions despite transformations, like changes in viewpoint or actor, that substantially alter the visual appearance of a scene. This ability to generalize across complex transformations is a hallmark of human visual intelligence. Advances in understanding action recognition at the neural level have not always translated into precise accounts of the computational principles underlying what representations of action sequences are constructed by human visual cortex. Here we test the hypothesis that invariant action discrimination might fill this gap. Recently, the study of artificial systems for static object perception has produced models, Convolutional Neural Networks (CNNs), that achieve human level performance in complex discriminative tasks. Within this class, architectures that better support invariant object recognition also produce image representations that better match those implied by human and primate neural data. However, whether these models produce representations of action sequences that support recognition across complex transformations and closely follow neural representations of actions remains unknown. Here we show that spatiotemporal CNNs accurately categorize video stimuli into action classes, and that deliberate model modifications that improve performance on an invariant action recognition task lead to data representations that better match human neural recordings. Our results support our hypothesis that performance on invariant discrimination dictates the neural representations of actions computed in the brain. These results broaden the scope of the invariant recognition framework for understanding visual intelligence from perception of inanimate objects and faces in static images to the study of human perception of action sequences.
Pustular psoriasis of pregnancy: current perspectives

Pustular psoriasis of pregnancy (PPP) is a life-threatening condition for both the pregnant mother and fetus, and must be efficiently and accurately diagnosed and treated. This condition has historically been classified as a unique, separate dermatosis of pregnancy. However, current opinion and data suggest that it may be a variant of generalized pustular psoriasis. PPP typically occurs in the third trimester and is characterized by widespread coalescent pustules, desquamation, and systemic symptoms. Clinical features and histopathologic evaluation aid in diagnosis. Treatments during pregnancy include high-dose corticosteroids, cyclosporine, narrow-band ultraviolet B radiation, infliximab, granulocyte and monocyte adsorptive apheresis, and systemic antibiotics. Both the mother and fetus should be closely monitored with appropriate laboratory studies for the duration of the pregnancy and postpartum.
ProQ3D: improved model quality assessments using deep learning

Summary: Protein quality assessment is a long‐standing problem in bioinformatics. For more than a decade we have developed state‐of‐art predictors by carefully selecting and optimising inputs to a machine learning method. The correlation has increased from 0.60 in ProQ to 0.81 in ProQ2 and 0.85 in ProQ3 mainly by adding a large set of carefully tuned descriptions of a protein. Here, we show that a substantial improvement can be obtained using exactly the same inputs as in ProQ2 or ProQ3 but replacing the support vector machine by a deep neural network. This improves the Pearson correlation to 0.90 (0.85 using ProQ2 input features). Availability and Implementation: ProQ3D is freely available both as a webserver and a stand‐alone program at http://proq3.bioinfo.se/ Contact: arne@bioinfo.se Supplementary information: Supplementary data are available at Bioinformatics online.
Thermal Infrared Signatures and Heat Fluxes of Sea Foam

Abstract : The goal of this research is to quantitatively characterize the temperature change of natural sea foam in the wake of breaking surface waves as observed with thermal imaging. Measurements in a set of laboratory experiments were carried out to verify or refute the supposition thatenhanced evaporative-cooling is responsible for this phenomenon. A control volume technique was successfully used to estimate the heat flux from foam and foam free surfaces in alaboratory wind tunnel. The results show that foam enhances the heat flux from seawater by afactor of 3-5. The surface thermal signature of the sea foam observed using long- and mid wave thermal cameras, reveals an unexpected mottled texture. We infer this is due to the cooled surface fluid draining from large bubbles to the extent that they are thin enough to transmit IR radiation from warmer bulk water and foam below. A parametric bulk flux method for the heat flux due to foam and analysis of the remote sensing signature are key results of this project.
Age differences in suggestibility to contradictions of demonstrated knowledge: the influence of prior knowledge

ABSTRACT People maintain intact general knowledge into very old age and use it to support remembering. Interestingly, when older and younger adults encounter errors that contradict general knowledge, older adults suffer fewer memorial consequences: Older adults use fewer recently-encountered errors as answers for later knowledge questions. Why do older adults show this reduced suggestibility, and what role does their intact knowledge play? In three experiments, I examined suggestibility following exposure to errors in fictional stories that contradict general knowledge. Older adults consistently demonstrated more prior knowledge than younger adults but also gained access to even more across time. Additionally, they did not show a reduction in new learning from the stories, indicating lesser involvement of episodic memory failures. Critically, when knowledge was stably accessible, older adults relied more heavily on that knowledge compared to younger adults, resulting in reduced suggestibility. Implications for the broader role of knowledge in aging are discussed.
Light Entrained Rhythmic Gene Expression in the Sea Anemone Nematostella vectensis: The Evolution of the Animal Circadian Clock

Background Circadian rhythms in behavior and physiology are the observable phenotypes from cycles in expression of, interactions between, and degradation of the underlying molecular components. In bilaterian animals, the core molecular components include Timeless-Timeout, photoreceptive cryptochromes, and several members of the basic-loop-helix-Per-ARNT-Sim (bHLH-PAS) family. While many of core circadian genes are conserved throughout the Bilateria, their specific roles vary among species. Here, we identify and experimentally study the rhythmic gene expression of conserved circadian clock members in a sea anemone in order to characterize this gene network in a member of the phylum Cnidaria and to infer critical components of the clockwork used in the last common ancestor of cnidarians and bilaterians. Methodology/Principal Findings We identified homologs of circadian regulatory genes in the sea anemone Nematostella vectensis, including a gene most similar to Timeout, three cryptochromes, and several key bHLH-PAS transcription factors. We then maintained N. vectensis either in complete darkness or in a 12 hour light: 12 hour dark cycle in three different light treatments (blue only, full spectrum, blue-depleted). Gene expression varied in response to light cycle and light treatment, with a particularly strong pattern observed for NvClock. The cryptochromes more closely related to the light-sensitive clade of cryptochromes were upregulated in light treatments that included blue wavelengths. With co-immunoprecipitation, we determined that heterodimerization between CLOCK and CYCLE is conserved within N. vectensis. Additionally, we identified E-box motifs, DNA sequences recognized by the CLOCK:CYCLE heterodimer, upstream of genes showing rhythmic expression. Conclusions/Significance This study reveals conserved molecular and functional components of the circadian clock that were in place at the divergence of the Cnidaria and Bilateria, suggesting the animal circadian clockwork is more ancient than previous data suggest. Characterizing circadian regulation in a cnidarian provides insight into the early origins of animal circadian rhythms and molecular regulation of environmentally cued behaviors.
Proton beam therapy for liver metastases from gastric cancer

Abstract Liver metastases from gastric cancer (LMGC) is a non-curable, fatal disease with a 5-year survival rate of <10%. Although various local treatments have been applied, their clinical utility has not been established. The purpose of this study was to investigate the safety and effectiveness of proton beam therapy (PBT) for the treatment of patients with LMGC. A total of nine patients (seven men, two women; aged 56–78 years) with LMGC who received PBT between 2002 and 2012 were retrospectively reviewed. Patients who had tumors confined to the liver were investigated, and patients who had extrahepatic tumors were excluded. Six of the patients had solitary tumors, and three patients had multiple tumors. The total irradiation dose was 64–77 Gy relative biological effectiveness (RBE), and three patients received concurrent chemotherapy. The overall and progression-free survival (OS and PFS) rates, local control (LC) rate, and adverse effects were investigated. All patients completed treatment without interruption, and late adverse effects of higher than Grade 3 were not observed. The OS rates at 1, 3 and 5 years were 100%, 78% and 56%, respectively (median, 5.5 years); the PFS rates were 67%, 40% and 40% (median, 2.6 years); and the LC rates were 89%, 71% and 71%. PBT was demonstrated to be a safe treatment, and the OS and PFS rates were not inferior to those for other types of local treatment. Therefore, PBT should be considered as an effective local treatment option for patients with LMGC.
Dietary inflammatory index and memory function: population-based national sample of elderly Americans

Abstract The objective of this study was to examine the association between dietary inflammatory potential and memory and cognitive functioning among a representative sample of the US older adult population. Cross-sectional data from the 2011–2012 and 2013–2014 National Health and Nutrition Examination Survey were utilised to identify an aggregate sample of adults 60–85 years of age (n 1723). Dietary inflammatory index (DII®) scores were calculated using 24-h dietary recall interviews. Three memory-related assessments were employed, including the Consortium to Establish a Registry for Alzheimer’s disease (CERAD) Word Learning subset, the Animal Fluency test and the Digit Symbol Substitution Test (DSST). Inverse associations were observed between DII scores and the different memory parameters. Episodic memory (CERAD) (b adjusted=−0·39; 95 % CI −0·79, 0·00), semantic-based memory (Animal Fluency Test) (b adjusted=−1·18; 95 % CI −2·17, −0·20) and executive function and working-memory (DSST) (b adjusted=−2·80; 95 % CI −5·58, −0·02) performances were lowest among those with the highest mean DII score. Though inverse relationships were observed between DII scores and memory and cognitive functioning, future work is needed to further explore the neurobiological mechanisms underlying the complex relationship between inflammation-related dietary behaviour and memory and cognition.
Proenkephalin and risk of developing chronic kidney disease: the Prevention of Renal and Vascular End-stage Disease study

Abstract Background: Proenkephalin (pro-ENK) was recently found to be associated with low estimated glomerular filtration rate (eGFR). The association of pro-ENK with urinary albumin excretion (UAE), another marker for chronic kidney disease (CKD), has not been investigated. We examined the association of pro-ENK with eGFR and UAE as markers of CKD. Methods: We included 4375 subjects of the Prevention of Renal and Vascular End-Stage Disease (PREVEND) study. CKDeGFR was defined as development of eGFR <60 ml/min/1.73 m2 and CKDUAE as albuminuria >30 mg/24 h. Results: Baseline median pro-ENK was 52.2 (IQR: 44.9–60.5) pmol/L. After a median follow-up of 8.4 (IQR: 7.9–8.9) years, 183 subjects developed CKDeGFR and 371 developed CKDUAE. The association of pro-ENK with CKDeGFR was modified by sex (Pinteraction < 0.1), in such a way that after adjustment, the association only remained significant in men (adjusted hazard ratio per SD increase in 10log-transformed pro-ENK, 1.65; 95% CI: 1.15–2.36) and not in women (0.83; 0.58–1.20). No significant association was observed between pro-ENK and CKDUAE risk (0.83; 0.58–1.20). Conclusions: High pro-ENK is associated with increased risk of CKDeGFR in men, but not in women. No association of pro-ENK with CKDUAE was observed. These results should be interpreted with caution, since residual confounding and potential overfitting of models could have influenced the results.
Adaptive Robot Second Language Tutoring for Children

Empirical evidence has demonstrated that learning with and from a physically present, interactive robot can be more effective than learning from classical on-screen media [6, 8]. In the L2TOR project wework on using the robot Nao to support second language learning, a problem that becomes increasingly important nowadays.We focus on preschool children in the age of 5-6yr, for whom it is crucial to develop adequate knowledge of the academic language as later educational success builds on it [4, 7].
Quality and Cost of Deterministic Network Calculus

Networks are integral parts of modern safety-critical systems and certification demands the provision of guarantees for data transmissions. Deterministic Network Calculus (DNC) can compute a worst-case bound on a data flow's end-to-end delay. Accuracy of DNC results has been improved steadily, resulting in two DNC branches: the classical algebraic analysis and the more recent optimization-based analysis. The optimization-based branch provides a theoretical solution for tight bounds. Its computational cost grows, however, (possibly super-)exponentially with the network size. Consequently, a heuristic optimization formulation trading accuracy against computational costs was proposed. In this article, we challenge optimization-based DNC with a new algebraic DNC algorithm. We show that: no current optimization formulation scales well with the network size and algebraic DNC can be considerably improved in both aspects, accuracy and computational cost. To that end, we contribute a novel DNC algorithm that transfers the optimization's search for best attainable delay bounds to algebraic DNC. It achieves a high degree of accuracy and our novel efficiency improvements reduce the cost of the analysis dramatically. In extensive numerical experiments, we observe that our delay bounds deviate from the optimization-based ones by only 1.142% on average while computation times simultaneously decrease by several orders of magnitude.
CHD1 loss sensitizes prostate cancer to DNA damaging therapy by promoting error-prone double-strand break repair

Background Deletion of the chromatin remodeler chromodomain helicase DNA-binding protein 1 (CHD1) is a common genomic alteration found in human prostate cancers (PCas). CHD1 loss represents a distinct PCa subtype characterized by SPOP mutation and higher genomic instability. However, the role of CHD1 in PCa development in vivo and its clinical utility remain unclear. Patients and methods To study the role of CHD1 in PCa development and its loss in clinical management, we generated a genetically engineered mouse model with prostate-specific deletion of murine Chd1 as well as isogenic CHD1 wild-type and homozygous deleted human benign and PCa lines. We also developed patient-derived organoid cultures and screened patients with metastatic PCa for CHD1 loss. Results We demonstrate that CHD1 loss sensitizes cells to DNA damage and causes a synthetic lethal response to DNA damaging therapy in vitro, in vivo, ex vivo, in patient-derived organoid cultures and in a patient with metastatic PCa. Mechanistically, CHD1 regulates 53BP1 stability and CHD1 loss leads to decreased error-free homologous recombination (HR) repair, which is compensated by increased error-prone non-homologous end joining (NHEJ) repair for DNA double-strand break (DSB) repair. Conclusions Our study provides the first in vivo and in patient evidence supporting the role of CHD1 in DSB repair and in response to DNA damaging therapy. We uncover mechanistic insights that CHD1 modulates the choice between HR and NHEJ DSB repair and suggest that CHD1 loss may contribute to the genomic instability seen in this subset of PCas.
Smoking and Tobacco-Free Policies in Women’s Residential Substance Use Disorder Treatment Facilities: A Community-Engaged Approach

Introduction The purpose of this study was to (1) describe the role of smoking in the lives of women in residential substance use disorder (SUD) treatment and (2) explore perceptions of the facilitators and barriers to tobacco-free policy among women in residential SUD treatment. Methods This was a community-engaged study using qualitative descriptive methods. We first recruited women in a residential SUD treatment facility to participate on a community research team. Interviews with staff (N = 10) and focus groups with clients (N = 42) were conducted using guides informed by the community research team. Interviews and focus groups were analyzed using content analysis. Results There were two themes related to the role of smoking in the women's lives: (1) smoking facilitates socialization and (2) smoking as a coping mechanism. There were three themes related to the benefits of tobacco-free policy: (1) improved health, (2) support for continued abstinence from a previous tobacco-free placement (eg, prison), and (3) less grounds up-keep. Barriers to tobacco-free policy included (1) lack of an alternative coping mechanism to smoking, (2) fear that a tobacco-free policy would drive clients away, and (3) anticipation of implementation challenges. Conclusions Many women in residential SUD treatment smoke, which they attribute to the fact that smoking is used to facilitate socialization and cope with stress. Future research is needed to develop and test messages to counter the misperception that smoking is an effective method to cope with stress. Ultimately, evidence-based tobacco-free policies are needed to reduce tobacco-related disease among women with SUDs. Implications To promote smoking cessation among women with substance use disorders through evidence-based tobacco policy, it is necessary to first understand the role of smoking in their lives as well as facilitators and barriers to tobacco-free policy in residential treatment facilities. Participants reported that smoking facilitated socialization and served as a coping mechanism. Tobacco-free policies have many benefits, including improved health, support for continued abstinence from a previous tobacco-free placement (eg, prison), and less grounds up-keep. Barriers include the lack of an alternative coping mechanism, fear that a tobacco-free policy would drive away clients and anticipation of implementation challenges. To reduce the burden of tobacco-related morbidity and mortality among women and their children, it is necessary to catalyze a culture change in behavioral health settings to prioritize the treatment of tobacco alongside treatment of other addictions.
Equivalent circuit characterization of resonant magnetic coupling for wireless transmission of electrical energy

This paper provides the accurate characterization of a wireless power transfer system consisting of two resonant air‐core coils mutually coupled in free space. The lumped‐circuit parameters of the equivalent circuit are determined with analytical formulas taken from the literature and validated by comparison with numerical simulations with a finite‐element computer code and with experiments. The parameters are determined taking as input only the geometry of the system (coil size and mutual distance, conductor radius, and turn distance) and the frequency. Once the lumped‐circuit parameters are known with good accuracy, the assessment of the power transfer system can be carried out by evaluating the current and voltage gains and efficiency for different system geometries, operating frequencies and load conditions. The Scilab programming environment was used to perform all the calculations. The characterization presented in this paper can then be considered as an effective tool in designing an efficient wireless power system. Copyright © 2012 John Wiley & Sons, Ltd.
Experimental and numerical strength assessment of stiffened plates subjected to severe non-uniform corrosion degradation and compressive load

ABSTRACT The objective of this work is to investigate experimentally and numerically the severe non-uniform corrosion degradation effect on the load carrying capacity of stiffened plates. Eight stiffened plates, which are initially corroded in real open sea conditions with different corrosion degradation levels, have been tested under compressive load. Different factors leading to a reduction of structural capacity have been investigated, including the material properties, degree of degradation, equivalent thickness and testing support conditions. The experimental results also showed to be very close to those estimated by the existing guideline procedure for a numerical evaluation of the ultimate strength, adjusted to be used for the severe corroded stiffened plates.