Miracle-dz/UniFAR-FTUs huggingface dataset:
Optimized Co-extraction and Quantification of DNA From Enteric Pathogens in Surface Water Samples Near Produce Fields in California

Pathogen contamination of surface water is a health hazard in agricultural environments primarily due to the potential for contamination of crops. Furthermore, pathogen levels in surface water are often unreported or under reported due to difficulty with culture of the bacteria. The pathogens are often present, but require resuscitation, making quantification difficult. Frequently, this leads to the use of quantitative PCR targeted to genes unique to the pathogens. However, multiple pathogen types are commonly in the same water sample, both gram + and gram –, leading to problems with DNA extraction. With Shiga toxin-producing Escherichia coli (STEC), Salmonella enterica and Listeria monocytogenes as target, a method was optimized to co-extract all three and quantify the level of each using droplet digital PCR (ddPCR). Multiplexed target genes in STEC were virulence genes, shiga toxin 2 (stx2) and hemolysin (ehx). Likewise, multiplexed targets in Listeria and Salmonella were the virulence genes listeriolysin (hly) and invasion protein A (invA). Water samples were processed using microbiological techniques for each of the pathogens and duplicate water samples were quantified by ddPCR. A significant correlation was found between culture and ddPCR results indicating detection primarily of culturable cells by ddPCR. Average virulence gene levels were 923, 23 k, 69 and 152 copies per sample for stx2, ehx, hly and invA, respectively. Additionally, stx2, ehx and inv levels were significantly correlated (P < 0.05, R = 0.34) with generic E. coli MPN levels in the duplicate samples. Indirect quantification with ddPCR will improve understanding of prevalence of the pathogens and may reduce risks associated with contaminated surface water.
Event-Based Control for Network Systems via Integral Quadratic Constraints

This paper investigates the event-based control for network systems. Edge-based approach is utilized to predict the value of edge state between two event instants. Different from the node-based approach, it can significantly reduce the communication burden at event instants. Based on the small gain theorem, the closed-loop system is expressed as the feedback interconnection of a linear time-invariant system and an operator. The operator describes the unstable component and has an upper bound in $L_{2}$ space and the control gain is designed, such that the feedback interconnection is stable. Furthermore, we adopt the integral quadratic constraints to describe the correlation between output and input of the operator. And the Kalman–Yakubovich–Popov Lemma is adopted to transform the infinite dimensional stability condition into one inequality. The designed event-triggering condition and distributed control law can ensure that a network system achieves synchronization. The effectiveness of the communication protocol and control strategy is illustrated by a numerical example.
Explicit group AOR method for solving elliptic partial differential equations

The explicit group overrelaxation methods for the numerical solution of the sparse linear systems derived from the discretisation of self-adjoint elliptic partial differential equations have been presented (Yousif & Evans, 1986) and has been shown to be computationally superior in comparison with the implicit 1-line and 2-line block succsessive overrelaxation (SOR) iterative methods. In this work a new explicit 4-point group accelerated overrelaxation (Group AOR) iterative method is presented. A comparison with the point AOR method for the model problem shows the computational advantages of the new technique.
Oxytocin regulates reunion affiliation with a pairmate following social separation in marmosets

While separation from significant social partners produces a host of neurobiological and behavioral perturbations, including behavioral distress and increased glucocorticoid production, positive social interactions upon reunion are critical for the reestablishment of normative relationship dynamics and the attenuation of the biobehavioral stress response. The hormone oxytocin has critical and pervasive roles in reproductive and behavioral processes across the lifespan, and plays a particularly prominent role in social bonding. In this study, we examined the extent that oxytocin modulates interactions with a pairmate following separation challenges that varied in both social context (isolation; separation) and duration (long; short), in marmosets. We demonstrated that the impact of pharmacological manipulations of the oxytocin system on the expression of affiliation upon reunion depended on both the context and duration of the separation challenge. Specifically, marmosets treated with an oxytocin antagonist spent less time in proximity with their pairmate upon reunion following a long‐separation challenge. During the short‐separation challenge, marmosets engaged in more social gaze when separated with an opposite‐sex stranger, but not when separated with their mate. Furthermore, marmosets that received the most social gaze from opposite‐sex strangers spent the most time in proximity with their long‐term mate upon reunion. We also showed that marmosets treated with an OT agonist received increased levels of gaze from opposite‐sex strangers, but not from their mate. Overall, these results suggest that marmosets are sensitive to the nature of the social interactions during separation, and subsequently alter their expression of affiliation upon reunion with their long‐term mate. These findings further implicate oxytocin as a bond‐enhancing molecule that regulates the reestablishment of normative levels of affiliation with a mate following separation, and add to the emerging literature that suggests the OT system underlies critical behavioral processes that contribute to the preservation of long‐lasting social bonds.
In vitro evaluation of gel‐encapsulated adipose derived stem cells: Biochemical cues for in vivo peripheral nerve repair

Adipose‐derived stem cells (ASC) are becoming one of the most exploited cells in peripheral nerve repair. They are fast‐growing and able to protect neurons from apoptosis; they can reduce post‐injury latency and the risk of muscle atrophy. This study evaluates laminin‐loaded fibrin gel as an ASC‐carrying scaffold for nerve repair. In vitro, ASC retained their proliferative activity but showed significant increase in proliferation rate when encapsulated in gels with low laminin concentrations (i.e., 1 μg/mL). We observed a linear decrease of ASC proliferation rate with increasing laminin concentration from 1 to 100 μg/mL. We next examined the effect of the ASC‐carrying fibrin gels on in vitro dorsal root ganglia (DRG) neurite extension, then in vivo sciatic nerve regeneration in adult rats. The ASC‐carrying gel was embedded in 15‐mm‐long, 1.5‐mm‐diameter polydimethylsiloxane regenerative conduits for in vivo evaluation. At 8‐week post implantation, robust regeneration was observed across the long gap. Taken together, these results suggest ASC‐carrying gels are a potential path to improve the efficacy of nerve regeneration through artificial guidance conduits and electrode nerve interfaces.
Multicenter evaluation of a new closed system drug‐transfer device in reducing surface contamination by antineoplastic hazardous drugs

Purpose Results of a study to evaluate the effectiveness of a recently introduced closed system drug‐transfer device (CSTD) in reducing surface contamination during compounding and simulated administration of antineoplastic hazardous drugs (AHDs) are reported. Methods Wipe samples were collected from 6 predetermined surfaces in compounding and infusion areas of 13 U.S. cancer centers to establish preexisting levels of surface contamination by 2 marker AHDs (cyclophosphamide and fluorouracil). Stainless steel templates were placed over the 6 previously sampled surfaces, and the marker drugs were compounded and infused per a specific protocol using all components of the CSTD. Wipe samples were collected from the templates after completion of tasks and analyzed for both marker AHDs. Results Aggregated results of wipe sampling to detect preexisting contamination at the 13 study sites showed that overall, 66.7% of samples (104 of 156) had detectable levels of at least 1 marker AHD; subsequent testing after CSTD use per protocol found a sample contamination rate of 5.8% (9 of 156 samples). In the administration areas alone, the rate of preexisting contamination was 78% (61 of 78 samples); with use of the CSTD protocol, the contamination rate was 2.6%. Twenty‐six participants rated the CSTD for ease of use, with 100% indicating that they were satisfied or extremely satisfied. Conclusion A study involving a rigorous protocol and 13 cancer centers across the United States demonstrated that the CSTD reduced surface contamination by cyclophosphamide and fluorouracil during compounding and simulated administration. Participants reported that the CSTD was easy to use.
Effects of degree of pulmonary fissure completeness on major in-hospital outcomes after video-assisted thoracoscopic lung cancer lobectomy: a retrospective-cohort study

Background To evaluate the clinical significance of degree of pulmonary fissure completeness (PFC) on major in-hospital outcomes following video-assisted thoracoscopic (VATS) lobectomy for non-small-cell lung cancer (NSCLC). Materials and methods We carried out a single-center retrospective analysis on the prospectively maintained database at our unit between August 2014 and October 2015. Patients were divided into two groups based on their fissure sum average (FSA). Patients with FSA >1 (1< FSA ≤3) were considered to have incomplete pulmonary fissures (group A), while patients with FSA of 0–1 were considered to have complete pulmonary fissures (group B). Demographic differences in perioperative characteristics and surgical outcomes between these two groups were initially assessed. Then, a multivariate logistic-regression analysis was further conducted to identify the independent predictors for major in-hospital outcomes. Results A total of 563 patients undergoing VATS lobectomy for NSCLC were enrolled. There were 190 patients in group A and 373 patients in group B. The overall morbidity and mortality rates of our cohort were 30.6% and 0.5%, respectively. Group A patients had a significantly higher overall morbidity rate than group B patients (42.1% vs 24.7%, P<0.001). Both minor morbidity (40.5% vs 22%, P<0.001) and major morbidity (11.1% vs 5.6%, P=0.021) rates in group A patients were also significantly higher than group B patients. No significant difference was observed in mortality rate between these two groups (1.1% vs 0.3%, P=0.26). The incomplete degree of PFC was significantly correlated with length of stay and chest-tube duration (log-rank P<0.001) after surgery. Finally, the incomplete degree of PFC was found to be predictive of overall morbidity (OR 2.08, P<0.001), minor morbidity (OR 2.39, P<0.001), and major morbidity (OR 2.06, P=0.031) by multivariate logistic-regression analyses. Conclusion Degree of PFC is an excellent categorical predictor for both major and minor morbidity after VATS lobectomy for NSCLC.
Analysis and Design of a Ripple Reduction Chopper Bandpass Amplifier

A low-power low-noise chopper amplifier for biosensor applications is proposed. To tackle the inherent ripple artifacts, it employs a simple ripple reduction method using a bandpass amplifier. The chopper amplifier is a linear periodic time-varying system. The method of harmonic transfer matrix is used to derive the signal and the noise harmonic transfer functions, and the theoretical results are confirmed by simulation and measurement results. Fabricated in a 130-nm standard CMOS process, the proof-of-concept prototype occupies a chip area of 0.28 mm<sup>2</sup> and consumes <inline-formula> <tex-math notation="LaTeX">$3.3~\mu {\text{A}}$ </tex-math></inline-formula> from a 1.2-V supply. The input referred noise is only 43 nV/<inline-formula> <tex-math notation="LaTeX">$({\mathrm {Hz}})^{1/2}$ </tex-math></inline-formula>.
Hurricane Sandy Exposure Alters the Development of Neural Reactivity to Negative Stimuli in Children.

This study examined whether exposure to Hurricane Sandy-related stressors altered children's brain response to emotional information. An average of 8 months (Mage = 9.19) before and 9 months after (Mage = 10.95) Hurricane Sandy, 77 children experiencing high (n = 37) and low (n = 40) levels of hurricane-related stress exposure completed a task in which the late positive potential, a neural index of emotional reactivity, was measured in response to pleasant and unpleasant, compared to neutral, images. From pre- to post-Hurricane Sandy, children with high stress exposure failed to show the same decrease in emotional reactivity to unpleasant versus neutral stimuli as those with low stress exposure. Results provide compelling evidence that exposure to natural disaster-related stressors alters neural emotional reactivity to negatively valenced information.
Space Use of Bumblebees (Bombus spp.) Revealed by Radio-Tracking

Background Accurate estimates of movement behavior and distances travelled by animals are difficult to obtain, especially for small-bodied insects where transmitter weights have prevented the use of radio-tracking. Methodology/Principal Findings Here, we report the first successful use of micro radio telemetry to track flight distances and space use of bumblebees. Using ground surveys and Cessna overflights in a Central European rural landscape mosaic we obtained maximum flight distances of 2.5 km, 1.9 km and 1.3 km for Bombus terrestris (workers), Bombus ruderatus (worker), and Bombus hortorum (young queens), respectively. Bumblebee individuals used large areas (0.25–43.53 ha) within one or a few days. Habitat analyses of one B. hortorum queen at the landscape scale indicated that gardens within villages were used more often than expected from habitat availability. Detailed movement trajectories of this individual revealed that prominent landscape structures (e.g. trees) and flower patches were repeatedly visited. However, we also observed long (i.e. >45 min) resting periods between flights (B. hortorum) and differences in flower-handling between bumblebees with and without transmitters (B. terrestris) suggesting that the current weight of transmitters (200 mg) may still impose significant energetic costs on the insects. Conclusions/Significance Spatio-temporal movements of bumblebees can now be tracked with telemetry methods. Our measured flight distances exceed many previous estimates of bumblebee foraging ranges and suggest that travelling long distances to food resources may be common. However, even the smallest currently available transmitters still appear to compromise flower handling performance and cause an increase in resting behavior of bees. Future reductions of transmitter mass and size could open up new avenues for quantifying landscape-scale space use of insect pollinators and could provide novel insights into the behavior and requirements of bumblebees during critical life stages, e.g. when searching for mates, nest locations or hibernation sites.
Modulation of Human Immune Responses by Bovine Interleukin-10

Cytokines can be functionally active across species barriers. Bovine IL-10 has an amino acid sequence identity with human IL-10 of 76.8%. Therefore, the aim of this study was to evaluate whether bovine IL-10 has immunomodulatory activities on human monocytes and dendritic cells. Peripheral blood monocytes were isolated from healthy donors, and used directly or allowed to differentiate to dendritic cells under the influence of IL-4 and GM-CSF. Recombinant bovine IL-10 inhibited TLR induced activation of monocytes, and dose-dependently inhibited LPS-induced activation of monocyte-derived DCs comparable to human IL-10. By using blocking antibodies to either bovine IL-10 or the human IL-10 receptor it was demonstrated that inhibition of monocyte activation by bovine IL-10 was dependent on binding of bovine IL-10 to the human IL-10R. These data demonstrate that bovine IL-10 potently inhibits the activation of human myeloid cells in response to TLR activation. Bovine IL-10 present in dairy products may thus potentially contribute to the prevention of necrotizing enterocolitis and allergy, enhance mucosal tolerance induction and decrease intestinal inflammation and may therefore be applicable in infant foods and in immunomodulatory diets.
Hydrological Analysis Using Satellite Remote Sensing Big Data and CREST Model

Hydrological modeling significantly contributes to the understanding of catchment water balance and water resource management and mitigates negative impacts of flooding. Considering the advantages of satellite remote sensing big data and the coupled routing and excess storage (CREST) model, this paper investigates the hydrological modeling in the Shehong basin during 2006–2013. The results show that humid Shehong basin has main rainfalls in summer (From May to September). For the monthly average rainfall and streamflow, there is a remarkable increase (+52%) in discharge and a smaller increase (+18%) in rainfall in the second period (2010–2013) relative to the first period (2006–2009). The CREST model was calibrated using China gauge-based daily precipitation analysis for the period of 2006–2009, followed by a favorable performance with Nash-Sutcliffe coefficient efficiency (NSCE) of 0.77, correlation coefficient (CC) up to 0.88 and −11% Bias. The model validation shows an error metric with NSCE of 0.74, CC of 0.87 and −11.7% Bias. In terms of water balance modeling results at Shehong basin, the runoff and rainfall estimates from CREST model coincide well with the gauge observations, indicating the model captures the appropriate signature of soil moisture variability. Therefore, the satellite-based precipitation product is feasible in hydrological prediction, and the CREST models the interaction between surface and subsurface water flow process in the Shehong basin.
Impact of Preadmission Opioid Treatment on 1-Year Mortality Following Nonsurgical Intensive Care*

Objectives: Compare all-cause mortality following nonsurgical ICU admission for opioid users with nonusers. Design: Nationwide register-based cohort study. Setting: All 43 ICUs in Denmark (7,028,668 citizens cumulatively during the study period). The Danish National Health Service provides universal healthcare, guaranteeing equal access to healthcare along with partial reimbursement for prescribed drugs. Patients: All 118,388 nonsurgical patients admitted to an ICU from 2005 to 2014. Intervention: Patients were categorized according to timing of last redeemed opioid prescription before admission: current user (prior 0–30 d), recent user (prior 31–365 d), former user (prior 365+ d), or nonuser (no prescription since 1994). Measurements: All-cause mortality 0–30 days and 31–365 days following ICU admission was calculated using the Kaplan-Meier method. Crude and adjusted hazard ratios with 95% CIs were computed using Cox regression, comparing users with nonusers. Adjusted models included age, gender, socioeconomic factors, comedications, and comorbidity. Main Results: Fifteen percent of the patients were current opioid users, 15% recent users, 30% former users, and 40% nonusers. Zero- to 30-day mortality was 35% for current users, 29% for recent users, 24% for former users, and 21% for nonusers. After confounder adjustment, current users remained at elevated risk during the first 30 days following ICU admission (hazard ratio, 1.20; 95% CI, 1.15–1.24). No association remained for recent or former users. A similar pattern was evident for 31–365-day all-cause mortality: 24% for current users, 19% for recent users, 13% for former users, and 10% for nonusers. During 31–365 days of follow-up, both current users and recent users remained at elevated risk of mortality after adjustment (hazard ratio, 1.47; 95% CI, 1.39–1.55 and hazard ratio, 1.20; 95% CI, 1.13–1.27, respectively). Conclusions: Current opioid users experience increased mortality during the first year following ICU admission.
Hydraulic redistribution under moderate drought among English oak, European beech and Norway spruce determined by deuterium isotope labeling in a split-root experiment

Hydraulic redistribution (HR) of soil water through plant roots is a crucial phenomenon improving the water balance of plants and ecosystems. It is mostly described under severe drought, and not yet studied under moderate drought. We tested the potential of HR under moderate drought, hypothesizing that (H1) tree species redistribute soil water in their roots even under moderate drought and that (H2) neighboring plants are supported with water provided by redistributing plants. Trees were planted in split-root systems with one individual (i.e., split-root plant, SRP) having its roots divided between two pots with one additional tree each. Species were 2- to 4-year-old English oak (Quercus robur L.), European beech (Fagus sylvatica L.) and Norway spruce (Picea abies (L.) Karst). A gradient in soil water potential (ψsoil) was established between the two pots (-0.55 ± 0.02 MPa and -0.29 ± 0.03 MPa), and HR was observed by labeling with deuterium-enriched water. Irrespective of species identity, 93% of the SRPs redistributed deuterium enriched water from the moist to the drier side, supporting H1. Eighty-eight percent of the plants in the drier pots were deuterium enriched in their roots, with 61 ± 6% of the root water originating from SRP roots. Differences in HR among species were related to their root anatomy with diffuse-porous xylem structure in both beech and-opposing the stem structure-oak roots. In spruce, we found exclusively tracheids. We conclude that water can be redistributed within roots of different tree species along a moderate ψsoil gradient, accentuating HR as an important water source for drought-stressed plants, with potential implications for ecohydrological and plant physiological sciences. It remains to be shown to what extent HR occurs under field conditions in Central Europe.
Inhibition of Calcium-Dependent Protein Kinase 1 (CDPK1) In Vitro by Pyrazolopyrimidine Derivatives Does Not Correlate with Sensitivity of Cryptosporidium parvum Growth in Cell Culture

ABSTRACT Cryptosporidiosis is a serious diarrheal disease in immunocompromised patients and malnourished children, and treatment is complicated by a lack of adequate drugs. Recent studies suggest that the natural occurrence of a small gatekeeper residue in serine threonine calcium-dependent protein kinase 1 (CDPK1) of Cryptosporidium parvum might be exploited to target this enzyme and block parasite growth. Here were explored the potency with which a series of pyrazolopyrimidine analogs, which are selective for small gatekeeper kinases, inhibit C. parvum CDPK1 and block C. parvum growth in tissue culture in vitro. Although these compounds potently inhibited kinase activity in vitro, most had no effect on parasite growth. Moreover, among those that were active against parasite growth, there was a very poor correlation with their 50% inhibitory concentrations against the enzyme. Active compounds also had no effect on cell invasion, unlike the situation in Toxoplasma gondii, where these compounds block CDPK1, prevent microneme secretion, and disrupt cell invasion. These findings suggest that CPDK1 is not essential for C. parvum host cell invasion or growth and therefore that it is not the optimal target for therapeutic intervention. Nonetheless, several inhibitors with low micromolar 50% effective concentrations were identified, and these may affect other essential targets in C. parvum that are worthy of further exploration.