Miracle-dz/UniFAR-FTUs huggingface dataset:
Subnational regional inequality in access to improved drinking water and sanitation in Indonesia: results from the 2015 Indonesian National Socioeconomic Survey (SUSENAS)

ABSTRACT Background: Universal and equitable access to safe and affordable drinking water and adequate sanitation and hygiene in Indonesia are vital to ensure healthy lives and promote well-being for all at all ages. Objectives: To quantify subnational regional inequality in access to improved drinking water and sanitation in Indonesia. Methods: Data about access to improved drinking water and sanitation were derived from the 2015 Indonesian National Socioeconomic Survey (SUSENAS) and disaggregated by 510 districts across the 34 provinces of Indonesia. Two summary measures of inequality, mean difference from mean and weighted index of disparity, were calculated to quantify within-province absolute and relative inequality, respectively. Results: While the majority of Indonesian households had access to improved drinking water (71.0%) and sanitation (62.1%), there were large variations between and within provinces. Access to improved drinking water ranged from 93.4% in DKI Jakarta to 41.1% in Bengkulu, and access to improved sanitation ranged from 89.3% in Jakarta to 23.9% in East Nusa Tenggara. Provinces with similar numbers of districts and similar overall averages showed variable levels of absolute and/or relative inequality. Certain districts reported very low levels of access to improved drinking water and/or sanitation. Conclusions: There are inequalities in access to improved drinking water and sanitation by subnational region in Indonesia. Monitoring within-country inequality in these indicators serves to identify underserved areas, and is useful for developing approaches to improve inequalities in access that can help Indonesia make progress towards the 2030 Agenda for Sustainable Development.
PME and Other ESBL-Positive Multiresistant Pseudomonas aeruginosa Isolated from Hospitalized Patients in the Region of Kurdistan, Iraq.

Nosocomial infections occur worldwide and also in the Kurdistan region. Frequently patients colonized with multiresistant Pseudomonas aeruginosa isolates are encountered in many hospitals. As information is lacking with respect to the mechanisms of resistance responsible for the multiresistant character of the P. aeruginosa isolates and their genetic relationship, isolates were prospectively collected and characterized with respect to their mechanism of resistance. During 2012 and 2013, 81 P. aeruginosa isolates were collected from three teaching hospitals in the city of Erbil, Iraq. Susceptibility testing was performed using the VITEK-2 system. Isolates were screened for the presence of extended-spectrum β-lactamases (ESBLs) and for the presence of metallo β-lactamases (MBLs). The presence of serine carbapenemases was detected by PCR. The genetic relationship of the isolates was demonstrated by amplified fragment length polymorphism (AFLP). Susceptibility results revealed high rates of resistance against all classes of antibiotics except polymyxins. Genetic characterization demonstrated the presence of ESBL-genes, that is, blaVEB (30%) and blaPER (17%), also ESBL blaPME was detected in four isolates. AFLP typing revealed clonal spread of blaVEB, blaPER, and three clusters of blaOXA-10-positive isolates. Only one isolate was MBL (blaVIM) positive. Of a selected number of isolates (n = 11), whole-genome sequencing analysis revealed that these isolates belonged to "high-risk" MLSTs ST244, ST235, ST308, and ST654. This study reveals the presence and clonal spread of widely resistant high-risk clones of P. aeruginosa in Iraqi Kurdistan. As far as we are aware, this is the first report of multiple, polyclonal, PME producing P. aeruginosa outside the Arabian Peninsula.
Increased Postoperative Manual Knee Laxity at 2 Years Results in Inferior Long-term Subjective Outcome After Anterior Cruciate Ligament Reconstruction

Background: Increased postoperative rotatory knee laxity after anterior cruciate ligament (ACL) reconstruction may be associated with an increased risk of osteoarthritis and inferior subjective outcome, although long-term studies are lacking. In terms of anteroposterior knee laxity, this association has not yet been established. Purpose/Hypothesis: The purpose was to investigate whether postoperative knee laxity is associated with inferior long-term outcome in patients who have undergone ACL reconstruction. The hypothesis was that increased laxity would cause an inferior long-term clinical and radiographic outcome. Study Design: Cohort study; Level of evidence, 3. Methods: A total of 193 patients underwent ACL reconstruction and were examined at both 2 and 16 years postoperatively. At the 2-year follow-up, knee laxity was tested by use of the Lachman test, the anterior drawer test, the pivot-shift test, and the KT-1000 arthrometer. Outcome variables examined at the 16-year follow-up involved a radiographic assessment of osteoarthritis, patient-reported outcome measurements, and the single-legged hop test. Results: At the long-term follow-up, 147 (76%) patients were examined. The mean follow-up period for the included patients was 16.4 ± 1.2 years. A negative Lachman test at 2 years resulted in a superior International Knee Documentation Committee (IKDC) score (76.3 ± 19.4 vs 67.8 ± 19.3, P < .05) and Lysholm score (85.2 ± 11.9 vs 76.9 ± 17.8, P < .05) at the 16-year follow-up. Correspondingly, a negative anterior drawer test at 2 years was associated with a superior IKDC score (75.3 ± 18.7 vs 62.9 ± 20.2, P < .05) and Lysholm score (84.1 ± 12.1 vs 72.6 ± 20.2, P < .05) at 16 years. A negative pivot-shift test resulted in a superior IKDC score (74.5 ± 18.8 vs 46.9 ± 17.8, P < .05), a superior Lysholm score (83.3 ± 13.4 vs 58.9 ± 23.0, P < .05), and an increased level of activity (Tegner activity scale, median [range]: 4 [1-10] vs 3 [0-5], P < .05). Osteoarthritis was overrepresented in patients with positive manual knee laxity tests, but the difference was not statistically significant. The KT-1000 arthrometer result was not correlated with any outcome variables assessed in this study. Conclusion: Increased manual anteroposterior and rotatory knee laxity 2 years after ACL reconstruction is associated with an inferior long-term subjective outcome.
Multivariate techniques enable a biochemical classification of children with autism spectrum disorder versus typically‐developing peers: A comparison and validation study

Abstract Autism spectrum disorder (ASD) is a developmental disorder which is currently only diagnosed through behavioral testing. Impaired folate‐dependent one carbon metabolism (FOCM) and transsulfuration (TS) pathways have been implicated in ASD, and recently a study involving multivariate analysis based upon Fisher Discriminant Analysis returned very promising results for predicting an ASD diagnosis. This article takes another step toward the goal of developing a biochemical diagnostic for ASD by comparing five classification algorithms on existing data of FOCM/TS metabolites, and also validating the classification results with new data from an ASD cohort. The comparison results indicate a high sensitivity and specificity for the original data set and up to a 88% correct classification of the ASD cohort at an expected 5% misclassification rate for typically‐developing controls. These results form the foundation for the development of a biochemical test for ASD which promises to aid diagnosis of ASD and provide biochemical understanding of the disease, applicable to at least a subset of the ASD population.
Meropenem synovial fluid concentrations after intravenous regional limb perfusion in standing horses

OBJECTIVE To determine meropenem concentrations in radiocarpal (RC) joint fluid and plasma after intravenous regional limb perfusion (IVRLP). STUDY DESIGN In vivo experimental study. ANIMALS Nine healthy adult mares. METHODS Meropenem (500 mg) was injected in the forelimb of standing sedated horses via IVRLP with a pneumatic tourniquet inflated to 400 mmHg. Synovial fluid was collected from RC joints at 0, 0.5, 1, 2, 4, 6, 8, 12, and 18 hours after meropenem injection. Blood samples were collected from the jugular vein at the same time points and at 5 and 15 minutes following injection. Meropenem concentrations were determined by using a microbiological bioassay. RESULTS Median synovial fluid concentrations reached a time of maximum synovial fluid concentration 0.5 hours after IVRLP. Synovial fluid concentrations varied greatly, with a mean maximum synovial fluid concentration of 25.6 µg/mL (range, below limit of quantitation to 75.5). Concentrations remained above the breakpoint for susceptibility (1 µg/mL) for 3 hours (last nonzero concentration measured, median) and 4.1 hours (predicted, mean). Concentrations >6 µg/mL were measured for 2 hours (observed, median) and 1.7 hours (predicted, mean). Six horses had mild swelling at the injection site. CONCLUSION Administration of 500 mg meropenem resulted in highly variable concentrations between horses and achieved levels above clinically relevant minimum inhibitory concentration for a minor portion of a once-daily dosing interval. CLINICAL SIGNIFICANCE If time-dependent pharmacodynamics apply, IVRLP with 500 mg of meropenem may be ineffective and would likely promote resistance.
Presence of anti-Müllerian hormone (AMH) during follicular development in the porcine ovary

Background Anti-Müllerian hormone (AMH) is expressed by granulosa cells of developing follicles and plays an inhibiting role in the cyclic process of follicular recruitment by determining follicle-stimulating hormone threshold levels. Knowledge of AMH expression in the porcine ovary is important to understand the reproductive efficiency in female pigs. Research aim In the present study we investigated the expression of AMH during follicular development in prepubertal and adult female pigs by immunohistochemistry, laser capture micro-dissection and RT-qPCR. Results and conclusion Although in many aspects the immunohistochemical localization of AMH in the porcine ovary does not differ from other species, there are also some striking differences. As in most species, AMH appears for the first time during porcine follicular development in the fusiform granulosa cells of recruited primordial follicles and continues to be present in granulosa cells up to the antral stage. By the time follicles reach the pre-ovulatory stage, AMH staining intensity increases significantly, and both protein and gene expression is not restricted to granulosa cells; theca cells now also express AMH. AMH continues to be expressed after ovulation in the luteal cells of the corpus luteum, a phenomenon unique to the porcine ovary. The physiological function of AMH in the corpus luteum is at present not clear. One can speculate that it may contribute to the regulation of the cyclic recruitment of small antral follicles. By avoiding premature exhaustion of the ovarian follicular reserve, AMH may contribute to optimization of reproductive performance in female pigs.
Computing Integer Sequences: Filtering vs Generation (Functional Pearl)

As a report of a teaching experience, we analyse Haskell programs computing two integer sequences: the Hamming sequence and the Ulam sequence. For both of them, we investigate two strategies of computation: the first is based on filtering out those natural numbers that do not belong to the sequence, whereas the second is based on the direct generation of num- bers that belong to the sequence. Advocating cross-fertilisation among ideas emerging when programming in different programming paradigms, in the background, we sketch out some considerations about corresponding C programs solving the same two problems.
Migration of Type III Secretion System Transcriptional Regulators Links Gene Expression to Secretion

ABSTRACT Many plant-pathogenic bacteria of considerable economic importance rely on type III secretion systems (T3SSs) of the Hrc-Hrp 1 family to subvert their plant hosts. T3SS gene expression is regulated through the HrpG and HrpV proteins, while secretion is controlled by the gatekeeper HrpJ. A link between the two mechanisms was so far unknown. Here, we show that a mechanistic coupling exists between the expression and secretion cascades through the direct binding of the HrpG/HrpV heterodimer, acting as a T3SS chaperone, to HrpJ. The ternary complex is docked to the cytoplasmic side of the inner bacterial membrane and orchestrates intermediate substrate secretion, without affecting early substrate secretion. The anchoring of the ternary complex to the membranes potentially keeps HrpG/HrpV away from DNA. In their multiple roles as transcriptional regulators and gatekeeper chaperones, HrpV/HrpG provide along with HrpJ potentially attractive targets for antibacterial strategies. IMPORTANCE On the basis of scientific/economic importance, Pseudomonas syringae and Erwinia amylovora are considered among the top 10 plant-pathogenic bacteria in molecular plant pathology. Both employ type III secretion systems (T3SSs) of the Hrc-Hrp 1 family to subvert their plant hosts. For Hrc-Hrp 1, no functional link was known between the key processes of T3SS gene expression and secretion. Here, we show that a mechanistic coupling exists between expression and secretion cascades, through formation of a ternary complex involving the T3SS proteins HrpG, HrpV, and HrpJ. Our results highlight the functional and structural properties of a hitherto-unknown complex which orchestrates intermediate T3SS substrate secretion and may lead to better pathogen control through novel targets for antibacterial strategies. IMPORTANCE On the basis of scientific/economic importance, Pseudomonas syringae and Erwinia amylovora are considered among the top 10 plant-pathogenic bacteria in molecular plant pathology. Both employ type III secretion systems (T3SSs) of the Hrc-Hrp 1 family to subvert their plant hosts. For Hrc-Hrp 1, no functional link was known between the key processes of T3SS gene expression and secretion. Here, we show that a mechanistic coupling exists between expression and secretion cascades, through formation of a ternary complex involving the T3SS proteins HrpG, HrpV, and HrpJ. Our results highlight the functional and structural properties of a hitherto-unknown complex which orchestrates intermediate T3SS substrate secretion and may lead to better pathogen control through novel targets for antibacterial strategies.
Mode selection considering fairness in D2D‐enabled cellular networks

In this paper, we consider the problem of mode selection, resource allocation, and power control for device‐to‐device (D2D) communications in cellular networks. We propose optimization frameworks based on max‐min fairness and proportional fairness where cellular and D2D links share the cellular resources. The optimization problem is solved in different resource sharing modes (ie, cellular, overlay, and underlay), and the mode leading to the highest optimal value is selected in the system. We further propose a two‐stage mode selection scheme based on channel quality in which the resource partitioning is expressed in closed form. We compare the performance of the proposed schemes with that of optimization framework based on sum‐rate and no‐mode selection scheme. The numerical results indicate that cellular and D2D links achieve higher rates in proportional fairness and max‐min fairness schemes compared to no‐mode selection scheme. While the rate improvement of D2D link is more significant in sum‐rate optimization, the cellular link may achieve lower rate in this scheme compared to other methods including the no‐mode selection scheme. The results also reveal that the rates of cellular and D2D links in channel quality scheme can vary within the range of rates obtained in max‐min and sum‐rate optimization frameworks.
Trustingly bewildered. How first-year medical students make sense of their learning experience in a traditional, preclinical curriculum

ABSTRACT Background: Traditional preclinical curricula based on memorization of scientific facts constitute learning environments which may negatively influence both factual understanding and professional identity development in medical students. Little is known of how students themselves experience and interpret such educational milieus.Objective: To investigate first-year medical students’ view of the physician role, and their perception of the relevance and quality of teaching in a science-based preclinical curriculum. Design: Focus group interviews with thematic text analysis. Results: Students portrayed the good physician as communicative, humble, and open, combining biomedical knowledge and moral strength. When asked how medical school supported the development of such characteristics, two partly contradictory discourses emerged. The critical discourse identified decontextualized knowledge, poor pedagogy, lack of critical thinking, and contact with faculty. Students who voiced critical comments also articulated trust that the system would provide the competence they needed, that basic biological knowledge is needed before clinical practice, and that being on your own conveys freedom and responsibility, and helps you grow up. Conclusion: Trust in the educational system, within a substandard learning environment, created cognitive dissonance that students resolved through rationalization, whereby they negated that factual overload and lack of relevance, reflection, and personal feedback was problematic. The cost of this mechanism is possibly that inferior teaching is perceived as normal, necessary, and good enough. If so, these future physicians’ ability to critically evaluate and create quality in medical education and practice, may be weakened.
Self-Reference Effect and Self-Reference Recollection Effect for Trait Adjectives in Amnestic Mild Cognitive Impairment

Abstract Objectives: The self-reference effect (SRE), enhanced memory for self-related information, has been studied in healthy young and older adults but has had little investigation in people with age-related memory disorders, such as amnestic mild cognitive impairment (aMCI). Self-referential encoding may help to improve episodic memory in aMCI. Additionally, self-referential processing has been shown to benefit recollection, the vivid re-experiencing of past events, a phenomenon that has been termed the self-reference recollection effect (SRRE; Conway & Dewhurst, 1995). Furthermore, it remains unclear whether the valence of stimuli influences the appearance of the SRE and SRRE. Methods: The current study investigated the SRE and SRRE for trait adjective words in 20 individuals with aMCI and 30 healthy older adult controls. Ninety trait adjective words were allocated to self-reference, semantic, or structural encoding conditions; memory was later tested using a recognition test. Results: While healthy older adults showed a SRE, individuals with aMCI did not benefit from self-referential encoding over and above that of semantic encoding (an effect of “deep encoding”). A similar pattern was apparent for the SRRE; healthy controls showed enhanced recollection for words encoded in the self-reference condition, while the aMCI group did not show specific benefit to recollection for self-referenced over semantically encoded items. No effects of valence were found. Conclusions: These results indicate that while memory for trait adjective words can be improved in aMCI with deep encoding strategies (whether self-reference or semantic), self-referencing does not provide an additional benefit. (JINS, 2018, 24, 821–832)
Computational Models of Emotion Inference in Theory of Mind: A Review and Roadmap

Abstract Research on social cognition has fruitfully applied computational modeling approaches to explain how observers understand and reason about others’ mental states. By contrast, there has been less work on modeling observers’ understanding of emotional states. We propose an intuitive theory framework to studying affective cognition—how humans reason about emotions—and derive a taxonomy of inferences within affective cognition. Using this taxonomy, we review formal computational modeling work on such inferences, including causal reasoning about how others react to events, reasoning about unseen causes of emotions, reasoning with multiple cues, as well as reasoning from emotions to other mental states. In addition, we provide a roadmap for future research by charting out inferences—such as hypothetical and counterfactual reasoning about emotions—that are ripe for future computational modeling work. This framework proposes unifying these various types of reasoning as Bayesian inference within a common “intuitive Theory of Emotion. ” Finally, we end with a discussion of important theoretical and methodological challenges that lie ahead in modeling affective cognition.
Association between perioperative hyperoxia and cerebrovascular complications after laparotomy—A post‐hoc follow‐up study

Perioperative hyperoxia has been linked to increased long‐term mortality. Vasoconstrictive and cellular side effects to hyperoxia have been suggested to increase the risk of coronary and cerebral ischemia. The aim of this post‐hoc analysis of a large randomized trial was to compare the effects of 80% vs 30% perioperative oxygen on the long‐term risk of stroke or transient cerebral ischemia (TCI) in patients undergoing abdominal surgery.
Prognostic Role and Clinical Association of Tumor-Infiltrating Lymphocyte, Programmed Death Ligand-1 Expression with Neutrophil-Lymphocyte Ratio in Locally Advanced Triple-Negative Breast Cancer

Purpose Tumor-infiltrating lymphocyte (TIL), programmed death-ligand 1 (PD-L1) expression and neutrophil-to-lymphocyte ratio (NLR) is associated to immunogenicity and prognosis of breast cancer. We analyzed baseline NLR, changes of NLR, TIL, and PD-L1 during neoadjuvant chemotherapy (NAC) and their clinical implication in triple-negative breast cancer (TNBC). Materials and Methods Between January 2008 to December 2015, 358 TNBC patients were analyzed. Baseline NLR, 50 paired NLR (initial diagnosis, after completion of NAC) and 34 paired tissues (initial diagnosis, surgical specimen after completion of NAC) were collected. Changes of TIL, CD4, CD8, forkhead box P3 (FOXP3), and PD-L1 expression were assessed with immunohistochemical stain. Results Low NLR (≤ 3.16) was associated to superior survival (overall survival: 41.83 months vs. 36.5 months, p=0.002; disease-free survival [DFS]: 37.85 months vs. 32.14 months, p=0.032). Modest NLR change after NAC (–30% < NLR change < 100%) showed prolonged DFS (38.37 months vs. 22.37 months, p=0.015). During NAC, negative or negative conversion of tumor PD-L1 expression was associated to poor DFS (34.77 months vs. 16.03 months, p=0.037), and same or increased TIL showed trends for superior DFS, but without statistical significance. Positive tumor PD-L1 expression (H-score ≥ 5) in baseline or post-NAC tissue was associated to superior DFS (57.6 months vs. 12.5 months, p=0.001 and 53.3 months vs. 18.9 months, p=0.040). Positive stromal PD-L1 expression in baseline was also associated to superior DFS (50.2 months vs. 20.4 months, p=0.002). Conclusion In locally advanced TNBC, baseline NLR, changes of NLR during NAC was associated to survival. Baseline PD-L1 expression and changes of PD-L1 expression in tumor tissue during NAC also showed association to prognosis.