Miracle-dz/UniFAR-FTUs huggingface dataset:
Tropical tree diversity mediates foraging and predatory effects of insectivorous birds

Biodiversity affects the structure of ecological communities, but little is known about the interactive effects of diversity across multiple trophic levels. We used a large-scale forest diversity experiment to investigate the effects of tropical tree species richness on insectivorous birds, and the subsequent indirect effect on predation rates by birds. Diverse plots (four tree species) had higher bird abundance (61%), phylogenetic diversity (61%), and functional diversity (55%) than predicted based on single-species monocultures, which corresponded to higher attack rates on artificial caterpillars (65%). Tree diversity effects on attack rate were driven by complementarity among tree species, with increases in attack rate observed on all tree species in polycultures. Attack rates on artificial caterpillars were higher in plots with higher bird abundance and diversity, but the indirect effect of tree species richness was mediated by bird diversity, providing evidence that diversity can interact across trophic levels with consequences tied to ecosystem services and function.
Low aquaporin-2 excretion in the nephrotic syndrome: an escape from the vasopressin regulating effect

Purpose Experimental studies suggest that the nephrotic syndrome is associated with “vasopressin escape”, characterized by low aquaporin-2 (AQP2) expression in the collecting duct despite high vasopressin secretion. We investigated this phenomenon in patients with the nephrotic syndrome. Patients and methods We recruited 47 patients with proteinuric kidney disease who were distributed into the following four groups: 1) nephrotic syndrome with kidney dysfunction (n=10); 2) nephrotic syndrome with normal kidney function (n=16); 3) partial remission of nephrotic syndrome (n=10); and 4) minimal proteinuria (n=11). Nine healthy volunteers comprised a control group. Serum copeptin level (as a marker of vasopressin secretion) and urinary AQP2 were measured using ELISA. Results Nephrotic syndrome was associated with a significant increase in serum copeptin levels compared with those in the other groups (all P<0.05). In patients with nephrotic syndrome and a partial remission of nephrotic syndrome combined, there was more than a ten-fold decrease in the median urinary AQP2 excretion (0.03 ng/mL) compared with healthy volunteers (0.41 ng/mL; P<0.001) and more than a five-fold decrease compared with patients with minimal proteinuria (0.21 ng/mL; P<0.05). Unlike copeptin levels, the median urinary AQP2 excretion in patients with minimal proteinuria also decreased but less significantly than in those with nephrotic syndrome. There was a negative correlation between the urinary AQP2 excretion and daily proteinuria (R=−0.41; P=0.005). Conclusion Our clinical study was the first to demonstrate low AQP2 excretion in nephrotic syndrome that may indicate an escape from the vasopressin regulating effect.
Electricity Consumption and Load Profile Segmentation Analysis for Rural Micro Grid Customers in Tanzania

Understanding electricity consumption behavior of different groups of customers is important to ensure appropriate microgrid designs. This paper assesses segmentation among microgrid customers in Tanzania according to electricity consumption behavior. Using the k-means clustering algorithm, 821 customers are placed into clusters by mean daily electricity consumption and mean normalized load profiles. We divided customers into three distinct segments by daily consumption level: < 140, 140–450, and > 450Wh. We also found five distinct load profile clusters. Clusters with high daytime electricity use tend to be commercial customers that consume large amounts of electricity. Households exhibit large evening peaks and consume relatively small amounts of electricity. Four of five load profiles show distinct evening peaks in consumption and one shows high night time electricity use. Microgrid developers can use these clusters and customer segments either to optimize the load profile for a power system by mixing certain customer types, or optimize the power system design to a given customer base.
Genome-wide CRISPR-dCas9 screens in E. coli identify essential genes and phage host factors

High-throughput genetic screens are powerful methods to identify genes linked to a given phenotype. The catalytic null mutant of the Cas9 RNA-guided nuclease (dCas9) can be conveniently used to silence genes of interest in a method also known as CRISPRi. Here, we report a genome-wide CRISPR-dCas9 screen using a pool of ~ 92,000 sgRNAs which target random positions in the chromosome of E. coli. We first investigate the utility of this method for the prediction of essential genes and various unusual features in the genome of E. coli. We then apply the screen to discover E. coli genes required by phages λ, T4 and 186 to kill their host. In particular, we show that colanic acid capsule is a barrier to all three phages. Finally, cloning the library on a plasmid that can be packaged by λ enables to identify genes required for the formation of functional λ capsids. This study demonstrates the usefulness and convenience of pooled genome-wide CRISPR-dCas9 screens in bacteria in order to identify genes linked to a given phenotype.
Sleep Disturbance in Mild Cognitive Impairment and Association With Cognitive Functioning. A Case-Control Study

Objectives: The aims of the current study are to (1) report the frequency of specific sleep disturbance symptoms in Mild Cognitive Impairment (MCI) and cognitive healthy older persons; (2) examine whether overall poor sleep and specific sleep disturbance symptoms are more common in persons with MCI compared to cognitive healthy older controls and; (3) examine the association between sleep disturbances and performance in general and specific cognitive domains in persons with MCI and separately in cognitive healthy older persons. Methods: Data were collected at the Fondazione Ospedale San Camillo Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Venice, Italy as part of the European VPH-DARE@IT project. We included 69 persons with MCI (mean age 75.7; SD = 7.7) and 72 sex-matched cognitively healthy controls (mean age 71.8; SD = 7.0). Participants underwent extensive neuropsychological assessment and evaluation of subjective sleep performance with the Sleep Continuity in Alzheimer’s Disease Scale(SCADS). Results: A fifth of MCI patients (21.7%, n = 15) had poor sleep compared to 15.3% (n = 11) of cognitively healthy controls. MCI patients had a 3.2 higher odds of having poor sleep compared to cognitively healthy controls after adjustment for age, education, sex, and general cognitive functioning (Odds Ratio (OR) = 3.2; 95% Confidence Interval (CI) = 1.1–9.2). Persons who reported waking up twice or more during the night had higher odds of being MCI compared to those who never wake or wake only once (OR = 2.6; 95% CI = 1.1–6.1). In MCI patients, poor sleep was associated with better general cognitive functioning and short-term working memory, whereas in cognitive healthy older persons poor sleep was associated with impairment in episodic memory performance and executive functioning. Discussion: Our results confirm previous studies showing that sleep disturbances are common in MCI, and this may be due to an ongoing neurodegenerative process rather than a symptom of cognitive impairment. Future research with objective sleep measurements are needed in MCI as well as interventions to improve sleep with the aim of preventing cognitive decline.
WebCircRNA: Classifying the Circular RNA Potential of Coding and Noncoding RNA

Circular RNAs (circRNAs) are increasingly recognized to play crucial roles in post-transcriptional gene regulation including functioning as microRNA (miRNA) sponges or as wide-spread regulators, for example in stem cell differentiation. It is therefore highly relevant to identify if a transcript of interest can also function as a circRNA. Here, we present a user-friendly web server that predicts if coding and noncoding RNAs have circRNA isoforms and whether circRNAs are expressed in stem cells. The predictions are made by random forest models using sequence-derived features as input. The output scores are converted to fractiles, which are used to assess the circRNA and stem cell potential. The performances of the three models are reported as the area under the receiver operating characteristic (ROC) curve and are 0.82 for coding genes, 0.89 for long noncoding RNAs (lncRNAs) and 0.72 for stem cell expression. We present WebCircRNA for quick evaluation of human genes and transcripts for their circRNA potential, which can be essential in several contexts.
The Key Role of TNF-TNFR2 Interactions in the Modulation of Allergic Inflammation: A Review

Tumor necrosis factor-alpha (TNF) is a pleiotropic cytokine, which is thought to play a major role in the pathogenesis of inflammatory diseases, including allergy. TNF is produced at the early stage of allergen sensitization, and then continues to promote the inflammation cascade in the effector phase of allergic reactions. Consequently, anti-TNF treatment has been proposed as a potential therapeutic option. However, recent studies reveal anti-intuitive effects of TNF in the activation and proliferative expansion of immunosuppressive Tregs, tolerogenic DCs and MDSCs. This immunosuppressive effect of TNF is mediated by TNFR2, which is preferentially expressed by immunosuppressive cells. These findings redefine the role of TNF in allergic reaction, and suggest that targeting TNF-TNFR2 interaction itself may represent a novel strategy in the treatment of allergy.
Pain, agitation and delirium assessment and management in a community medical-surgical ICU: results from a prospective observational study and nurse survey

Background Delirium is a common manifestation in the intensive care unit (ICU) that is associated with increased mortality and morbidity. Guidelines suggested appropriate management of pain, agitation and delirium (PAD) is crucial in improving patient outcomes. However, the practice of PAD assessment and management in community hospitals is unclear and the mechanisms contributing to the potential care gap are unknown. Objectives This quality improvement initiative aimed to review the practice of PAD assessment and management in a community medical-surgical ICU (MSICU) and to explore the community MSICU nurses’ perceived comfort and satisfaction with PAD management in order to understand the mechanisms of the observed care gap and to inform subsequent quality improvement interventions. Methods We prospectively collected basic demographic data, clinical information and daily data on PAD process measures including PAD assessment and target Richmond Agitation-Sedation Scale (RASS) score ordered by intensivists on all patients admitted to a community MSICU for >24 hours over a 20-week period. All ICU nurses in the same community MSICU were invited to participate in an anonymous survey. Results We collected data on a total of 1101 patient-days (PD). 653 PD (59%), 861 PD (78%) and 439 PD (39%) had PAD assessment performed, respectively. Target RASS was ordered by the intensivists on 515 PD (47%). Our nurse survey revealed that 88%, 85% and 41% of nurses were comfortable with PAD assessment, respectively. Conclusions Delirium assessment was not routinely performed. This is partly explained by the discomfort nurses felt towards conducting delirium assessment. Our results suggested that improvement in nurse comfort with delirium assessment and management is needed in the community MSICU setting.
Knowledge Tracing Machines: Factorization Machines for Knowledge Tracing

Knowledge tracing is a sequence prediction problem where the goal is to predict the outcomes of students over questions as they are interacting with a learning platform. By tracking the evolution of the knowledge of some student, one can optimize instruction. Existing methods are either based on temporal latent variable models, or factor analysis with temporal features. We here show that factorization machines (FMs), a model for regression or classification, encompasses several existing models in the educational literature as special cases, notably additive factor model, performance factor model, and multidimensional item response theory. We show, using several real datasets of tens of thousands of users and items, that FMs can estimate student knowledge accurately and fast even when student data is sparsely observed, and handle side information such as multiple knowledge components and number of attempts at item or skill level. Our approach allows to fit student models of higher dimension than existing models, and provides a testbed to try new combinations of features in order to improve existing models.
Systematic Review on Resting-State EEG for Alzheimer's Disease Diagnosis and Progression Assessment

Alzheimer's disease (AD) is a neurodegenerative disorder that accounts for nearly 70% of the more than 46 million dementia cases estimated worldwide. Although there is no cure for AD, early diagnosis and an accurate characterization of the disease progression can improve the quality of life of AD patients and their caregivers. Currently, AD diagnosis is carried out using standardized mental status examinations, which are commonly assisted by expensive neuroimaging scans and invasive laboratory tests, thus rendering the diagnosis time consuming and costly. Notwithstanding, over the last decade, electroencephalography (EEG) has emerged as a noninvasive alternative technique for the study of AD, competing with more expensive neuroimaging tools, such as MRI and PET. This paper reports on the results of a systematic review on the utilization of resting-state EEG signals for AD diagnosis and progression assessment. Recent journal articles obtained from four major bibliographic databases were analyzed. A total of 112 journal articles published from January 2010 to February 2018 were meticulously reviewed, and relevant aspects of these papers were compared across articles to provide a general overview of the research on this noninvasive AD diagnosis technique. Finally, recommendations for future studies with resting-state EEG were presented to improve and facilitate the knowledge transfer among research groups.
Peritoneal NK cells are responsive to IL-15 and percentages are correlated with outcome in advanced ovarian cancer patients

The demonstration that ovarian carcinoma (OC) is an immunogenic disease, opens opportunities to explore immunotherapeutic interventions to improve clinical outcome. In this regard, NK cell based immunotherapy could be promising as it has been demonstrated that OC cells are susceptible to killing by cytokine-stimulated NK cells. Here, we evaluated whether percentage, phenotype, function and IL-15 responsiveness of ascites-derived natural killer (NK) cells is related to progression-free survival (PFS) and overall survival (OS) of advanced stage OC patients. Generally, a lower percentage of NK cells within the lymphocyte fraction was seen in OC ascites (mean 17.4 ± 2.7%) versus benign peritoneal fluids (48.1 ± 6.8%; p < 0.0001). Importantly, a higher CD56+ NK cell percentage in ascites was associated with a better PFS (p = 0.01) and OS (p = 0.002) in OC patients. Furthermore, the functionality of ascites-derived NK cells in terms of CD107a/IFN-γ activity was comparable to that of healthy donor peripheral blood NK cells, and stimulation with monomeric IL-15 or IL-15 superagonist ALT-803 potently improved their reactivity towards tumor cells. By showing that a higher NK cell percentage is related to better outcome in OC patients and NK cell functionality can be boosted by IL-15 receptor stimulation, a part of NK cell immunity in OC is further deciphered to exploit NK cell based immunotherapy.
Rationale of Probiotic Supplementation during Pregnancy and Neonatal Period

Probiotics are living microorganisms that confer a health benefit when administered in adequate amounts. It has been speculated that probiotics supplementation during pregnancy and in the neonatal period might reduce some maternal and neonatal adverse outcomes. In this narrative review, we describe the rationale behind probiotic supplementation and its possible role in preventing preterm delivery, perinatal infections, functional gastrointestinal diseases, and atopic disorders during early life.
Outcomes of Kidney Transplantation by Using the Technique of Renal Artery Anastomosis First

Introduction The surgical technique for kidney transplantation has been well established: the renal vein is anastomosed first, followed by renal artery anastomosis. Alternatively, the renal artery can be anastomosed first and then the renal vein for kidney transplantation. However, there is a lack of data on the outcomes of kidney transplantation by using this alternative approach. The objective of this paper was to review the outcomes of kidney transplant by using this approach. Methods A review of 205 consecutive kidney transplants was conducted. All kidney transplants were performed by doing renal artery anastomosis first and then the renal vein. Data were collected, including vascular/urological complications and kidney graft function. Results All transplants were performed successfully with no occurrence of renal artery/vein thrombosis and urine leakage. There were five cases of renal artery stenosis that were managed with endovascular intervention. There was no recurrence on follow-up. One ureteric stenosis required surgical reconstruction. Conclusions This alternative vascular anastomotic technique is efficient and safe. It avoids flip-flopping the kidney graft during the vessel anastomoses and may be more practical in minimally invasive surgery for a kidney transplant due to the space constraint.
Toward Arbitrary-Oriented Ship Detection With Rotated Region Proposal and Discrimination Networks

Ship detection from remote sensing images can provide important information for maritime reconnaissance and surveillance and is also a challenging task. Although previous detection methods including some advanced ones based on deep convolutional neural network expertize in detecting horizontal or nearly horizontal targets, they cannot give satisfying detection results for arbitrary-oriented ship detection. In this letter, we introduce a novel ship detection system that can detect arbitrary-oriented ships. In this method, a rotated region proposal networks (R2PN) is proposed to generate multiorientated proposals with ship orientation angle information. In R2PN, the orientation angles of bounding boxes are also regressed to make the inclined ship region proposals generated more accurately. For ship discrimination, a rotated region of interest pooling layer is adopted in the following classification subnetwork to extract discriminative features from such inclined candidate regions. The proposed whole ship detection system can be trained end to end. Experimental results conducted on our rotated ship data set and HRSD2016 benchmark demonstrate that our proposed method outperforms state-of-the-art approaches for the arbitrary-oriented ship detection task.
Asymmetrical Impedance Inverter for Quasi-Optical Bandpass Filters With Transmission Lines of Fixed Length

Quasi-optical (QO) filter design is commonly based on the direct coupled bandpass filter topology with distributed resonator elements. Conventionally, prototypes with symmetrical impedance inverters are employed during synthesis, and as a result, this leads to resonators with custom lengths across the filter. This can be impractical from a QO filter implementation perspective, since spacers of arbitrary thickness may not be readily available. In this paper, we propose a novel impedance inverter equivalent network, which allows the development of prototypes where transmission lines across the filter structure to have predefined fixed lengths. Based on this technique, we developed a fourth-order QO filter prototype that composed of 2-D periodic arrays with subwavelength features. Its performance is verified with free-space measurement, and the measured results show good agreement with both full-wave and circuit simulation. Thus, it is shown that the proposed impedance inverter circuit can simplify the implementation of QO filters of higher order.
Alterations of peritoneal transport characteristics in dialysis patients with ultrafiltration failure: tissue and capillary components.

BACKGROUND Ultrafiltration failure (UFF) in peritoneal dialysis (PD) patients is due to altered peritoneal transport properties leading to reduced capacity to remove excess water. Here, with the aim to establish the role of local alterations of the two major transport barriers, peritoneal tissue and capillary wall, we investigate changes in overall peritoneal transport characteristics in UFF patients in relation to corresponding local alterations of peritoneal tissue and capillary wall transport properties. METHODS Six-hour dwell studies using 3.86% glucose solutions and radioisotopically labelled serum albumin added to dialysate as a volume marker were analysed in 31 continuous ambulatory PD patients, 20 with normal ultrafiltration (NUF) and 11 with UFF. For each patient, the physiologically based parameters were evaluated for both transport barriers using the spatially distributed approach based on the individual intraperitoneal profiles of volume and concentrations of glucose, sodium, urea and creatinine. RESULTS UFF patients as compared with NUF patients had increased solute diffusivity in both barriers, peritoneal tissue and capillary wall, decreased tissue hydraulic conductivity and increased local lymphatic absorption and functional decrease in the fraction of the ultra-small pores. This resulted in altered distribution of fluid and solutes in the peritoneal tissue, and decreased penetration depths of fluid and solutes into the tissue in UFF patients. CONCLUSIONS Mathematical modelling using a spatially distributed approach for the description of clinical data suggests that alterations both in the capillary wall and in the tissue barrier contribute to UFF through their effect on transport and distribution of solutes and fluid within the tissue.
Anti-neuroinflammatory Effects of 12-Dehydrogingerdione in LPS-Activated Microglia through Inhibiting Akt/IKK/NF-κB Pathway and Activating Nrf-2/HO-1 Pathway

Ginger, one of worldwide consumed dietary spice, is not only famous as food supplements, but also believed to exert a variety of remarkable pharmacological activity as herbal remedies. In this study, a ginger constituent, 12-dehydrogingerdione (DHGD) was proven that has comparable anti-inflammatory activity with positive control 6-shogaol in inhibiting LPS-induced interleukin (IL)-6, tumor necrosis factor (TNF)-α, prostaglandin (PG) E2, nitric oxide (NO), inducible NO synthase (iNOS) and cyclooxygenase (COX)-2, without interfering with COX-1 in cultured microglial cells. Subsequent mechanistic studies indicate that 12-DHGD may inhibit neuro-inflammation through suppressing the LPS-activated Akt/IKK/NF-κB pathway. Furthermore, 12-DHGD markedly promoted the activation of NF-E2-related factor (Nrf)-2 and heme oxygenase (HO)-1, and we demonstrated that the involvement of HO-1 on the production of pro-inflammatory mediators such as NO and TNF-α by using a HO-1 inhibitor, Zinc protoporphyrin (Znpp). These results indicate that 12-DHGD may protect against neuro-inflammation by inhibiting Akt/IKK/IκB/NF-κB pathway and promoting Nrf-2/HO-1 pathway.