Miracle-dz/UniFAR-FTUs huggingface dataset:
Diagnosis, Treatment, and Prevention of Lyme Disease, Human Granulocytic Anaplasmosis, and Babesiosis: A Review.

IMPORTANCE Lyme disease, human granulocytic anaplasmosis (HGA), and babesiosis are emerging tick-borne infections. OBJECTIVE To provide an update on diagnosis, treatment, and prevention of tick-borne infections. EVIDENCE REVIEW Search of PubMed and Scopus for articles on diagnosis, treatment, and prevention of tick-borne infections published in English from January 2005 through December 2015. FINDINGS The search yielded 3550 articles for diagnosis and treatment and 752 articles for prevention. Of these articles, 361 were reviewed in depth. Evidence supports the use of US Food and Drug Administration-approved serologic tests, such as an enzyme immunoassay (EIA), followed by Western blot testing, to diagnose extracutaneous manifestations of Lyme disease. Microscopy and polymerase chain reaction assay of blood specimens are used to diagnose active HGA and babesiosis. The efficacy of oral doxycycline, amoxicillin, and cefuroxime axetil for treating Lyme disease has been established in multiple trials. Ceftriaxone is recommended when parenteral antibiotic therapy is recommended. Multiple trials have shown efficacy for a 10-day course of oral doxycycline for treatment of erythema migrans and for a 14-day course for treatment of early neurologic Lyme disease in ambulatory patients. Evidence indicates that a 10-day course of oral doxycycline is effective for HGA and that a 7- to 10-day course of azithromycin plus atovaquone is effective for mild babesiosis. Based on multiple case reports, a 7- to 10-day course of clindamycin plus quinine is often used to treat severe babesiosis. A recent study supports a minimum of 6 weeks of antibiotics for highly immunocompromised patients with babesiosis, with no parasites detected on blood smear for at least the final 2 weeks of treatment. CONCLUSIONS AND RELEVANCE Evidence is evolving regarding the diagnosis, treatment, and prevention of Lyme disease, HGA, and babesiosis. Recent evidence supports treating patients with erythema migrans for no longer than 10 days when doxycycline is used and prescription of a 14-day course of oral doxycycline for early neurologic Lyme disease in ambulatory patients. The duration of antimicrobial therapy for babesiosis in severely immunocompromised patients should be extended to 6 weeks or longer.
World Knowledge for Abstract Meaning Representation Parsing

In this paper we explore the role played by world knowledge in semantic parsing. We look at the types of errors that currently exist in a state-of-the-art Abstract Meaning Representation (AMR) parser, and explore the problem of how to integrate world knowledge to reduce these errors. We look at three types of knowledge from (1) WordNet hypernyms and super senses, (2) Wikipedia entity links, and (3) retraining a named entity recognizer to identify concepts in AMR. The retrained entity recognizer is not perfect and cannot recognize all concepts in AMR and we examine the limitations of the named entity features using a set of oracles. The oracles show how performance increases if it can recognize different subsets of AMR concepts. These results show improvement on multiple ﬁne-grained metrics, including a 6% increase in named entity F-score, and provide insight into the potential of world knowledge for future work in Abstract Meaning Representation parsing.
Cyclooxygenase-2-Derived Prostaglandins Mediate Cerebral Microcirculation in a Juvenile Ischemic Rat Model

Background and Purpose— We previously showed that the selective neuronal nitric oxide synthase inhibitor 7-nitroindazole (7-NI) increases cerebral microcirculation in a juvenile ischemic rat model. We address the roles of cyclooxygenase (COX)-elaborated prostaglandins in collateral recruitment and blood supply. Methods— Fourteen-day-old rats were subjected to ischemia–reperfusion and treated with either PBS or 7-NI (25 mg/kg) at the reperfusion onset. Six-keto-prostaglandin F1&agr; was measured using ELISA. COX-1 and COX-2 and prostaglandin terminal synthesizing enzymes were evaluated using reverse-transcriptase polymerase chain reaction and immunofluorescence. Microvascular blood flow indexes (artery diameter and capillaries number) were measured using sidestream dark-field videomicroscopy in PBS- and 7-NI-treated ischemic rats in the absence or presence of the COX-2 inhibitor NS-398 (5 mg/kg). Cell death was measured with the TUNEL (terminal transferase dUTP nick end labeling) assay and cleaved-caspase-3 immunostaining. Results— Six-keto-prostaglandin F1&agr; and COX-2, associated with a prostaglandin E synthase, were significantly increased in PBS- and 7-NI-treated animals 15 minutes and 1 hour after ischemia–reperfusion, respectively. In contrast and as compared with PBS, 7-NI significantly decreased prostacyclin synthase and cytosolic prostaglandins E synthase mRNA. Selective COX-2 inhibition significantly decreased blood flow indexes and significantly reversed the effects of 7-NI, including the number of TUNEL+- and cleaved-caspase-3+-nuclei. Conclusions— These results show that the juvenile rat brains mostly respond to ischemia by a COX-2-dependent prostaglandins production and suggest that the transcriptional responses observed under 7-NI facilitate and reorient COX-2-dependent prostaglandins production.
Genome-wide DNA hypomethylation and RNA:DNA hybrid accumulation in Aicardi–Goutières syndrome

Aicardi–Goutières syndrome (AGS) is a severe childhood inflammatory disorder that shows clinical and genetic overlap with systemic lupus erythematosus (SLE). AGS is thought to arise from the accumulation of incompletely metabolized endogenous nucleic acid species owing to mutations in nucleic acid-degrading enzymes TREX1 (AGS1), RNase H2 (AGS2, 3 and 4), and SAMHD1 (AGS5). However, the identity and source of such immunogenic nucleic acid species remain undefined. Using genome-wide approaches, we show that fibroblasts from AGS patients with AGS1-5 mutations are burdened by excessive loads of RNA:DNA hybrids. Using MethylC-seq, we show that AGS fibroblasts display pronounced and global loss of DNA methylation and demonstrate that AGS-specific RNA:DNA hybrids often occur within DNA hypomethylated regions. Altogether, our data suggest that RNA:DNA hybrids may represent a common immunogenic form of nucleic acids in AGS and provide the first evidence of epigenetic perturbations in AGS, furthering the links between AGS and SLE. DOI: http://dx.doi. org/10.7554/eLife.08007. 001
The Contribution of Muscle to Whole-Body Protein Turnover Throughout the Course of Burn Injury in Children

The physiologic response to trauma results in the efflux of large amounts of amino acids from skeletal muscle. This is extreme in large burn injuries. Protein kinetic studies, although useful in determining the rates of protein synthesis and breakdown, do not provide information about muscle loss. This study determined the contribution of muscle protein to whole-body protein breakdown in children throughout their course of burn injury. Children aged 0 to 18 years with initial burn size ≥30% TBSA underwent 15N glycine and 3 methylhistidine (3MH) analysis during three phases of care: A, early acute; B, wound closure; and C, convalescence. Muscle protein breakdown was estimated using a factor of 4.2 &mgr;mol 3MH per 1 g of mixed protein. Twenty-two patients with a mean of 54.5 ± 20.1% TBSA burn were studied. Protein balance did not change remarkably and remained positive by 2 g/kg during hospitalization. However, muscle protein breakdown dropped from 1.1 to 0.6 g/kg with wound closure (P < .0001), representing a decrease in the contribution of muscle protein to whole-body protein breakdown from 20 to 7%. Ten patients returned for a third measurement after discharge. Although protein turnover was high, muscle breakdown was consistent with 3MH values reported in healthy children. Serial determination of 3MH excretion is a simple way to track muscle catabolism throughout burn injury. Our data suggest that despite accelerated protein turnover, muscle catabolism significantly decreases with wound closure and begins to normalize around discharge. In convalescence, 3MH excretion is comparable with normal children.
Topical corticosteroids reverse the antiviral effect of topical cidofovir in the Ad5-inoculated New Zealand rabbit ocular model.

PURPOSE To determine how the addition of topical corticosteroids would affect the anti-adenoviral inhibitory effect of topical cidofovir (S-HPMPC) in the Ad5 New Zealand (Ad5/NZ) rabbit ocular model. METHODS In a series of experiments (two-eye design), Ad5-inoculated/NZ rabbits (10(6) pfu/eye) were treated with 1 of 3 treatment regimens. Group 1 was administered 1% cidofovir (CDV) twice a day for 3 days plus comfort tears four times a day for 14 days. Group 2 was administered 1% CDV twice a day for 3 days plus 1% Pred Forte four times a day for 14 days. Group 3 was administered vehicle twice a day for 3 days plus comfort tears four times a day for 14 days and served as the control. All eyes were evaluated for 21 days for serial eye titers, Ad5 positive eyes, and duration of Ad5 shedding. RESULTS Compared to control eyes in the Ad5/NZ rabbit ocular model, CDV alone demonstrated a significant antiviral inhibitory effect: reduced mean Ad5 eye titer during the early phase of infection (days 3 to 7), fewer Ad5-positive eyes during the early and late (days 9 to 21) phases of infection, and shortened duration of shedding. However, concomitant treatment with both Pred Forte and CDV significantly reversed the antiviral inhibitory activity of CDV: increased mean Ad5 eye titer, increased Ad5-positive eyes (early and late phases) and prolonged duration of shedding. CONCLUSIONS These experimental data further support the clinical development of cidofovoir as a topical antiviral agent, but they do not support a treatment regimen that includes a combination of topical corticosteroids and topical cidofovir as a desirable strategy for the treatment of symptomatic adenoviral ocular infection.
Long-term thermal stability tests at 1000 degree C of silica fiber Bragg grating made with ultrafast laser radiation

Using an ultrafast Ti:sapphire IR laser and a phase mask, fiber Bragg gratings (FBGs) with high thermal stability were fabricated in SMF-28 fiber for sensor applications and were subjected to long annealing tests at 1000 °C. FBGs that maintained more then 99.95 % reflectivity after several hundred hours at this temperature are demonstrated. The gratings perform well in cycling experiments up to 1000 °C and hysteresis in the wavelength response was not detected. The capability of this new type of FBG to be used for high temperature sensors is briefly discussed.
Effects of an Early Handling-Like Procedure and Individual Housing on Anxiety-Like Behavior in Adult C57BL/6J and DBA/2J Mice

Manipulations of rearing conditions have been used to examine the effects of early experience on adult behavior with varying results. Evidence suggests that postnatal days (PND) 15–21 are a time of particular susceptibility to environmental influences on anxiety-like behavior in mice. To examine this, we subjected C57BL/6J and DBA/2J mice to an early handling-like procedure. Pups were separated from dams from PND 12–20 for 30 minutes daily or received standard care. On PND 21, pups were weaned and either individually- or group- housed. On PND 60, anxiety-like behavior was examined on the elevated zero-maze. Although individually- housed animals took longer to enter an open quadrant of the maze, they spent more time in the open than group-housed animals. Additionally, we observed a trend of reduced anxiety-like behavior in C57BL/6J, but not DBA/2J mice that underwent the handling-like procedure.
Effect of Long-Term Vascular Care on Progression of Cerebrovascular Lesions: Magnetic Resonance Imaging Substudy of the PreDIVA Trial (Prevention of Dementia by Intensive Vascular Care)

Background and Purpose— This study aimed to evaluate the effect of a nurse-led multidomain cardiovascular intervention on white matter hyperintensity (WMH) progression and incident lacunar infarcts in community-dwelling elderly with hypertension. Methods— The preDIVA trial (Prevention of Dementia by Intensive Vascular Care) was an open-label, cluster-randomized controlled trial in community-dwelling individuals aged 70 to 78 years. General practices were assigned by computer-generated randomization to 6-year nurse-led, multidomain intensive vascular care or standard care. Of 3526 preDIVA participants, 195 nondemented participants with a systolic blood pressure ≥140 mm Hg were consecutively recruited to undergo magnetic resonance imaging at 2 to 3 and 5 to 6 years after baseline. WMH volumes were measured automatically, lacunar infarcts assessed visually, blinded to treatment allocation. Results— One hundred and twenty-six participants were available for longitudinal analysis (64 intervention and 62 control). Annual WMH volume increase in milliliter was similar for intervention (mean=0.73, SD=0.84) and control (mean=0.70, SD=0.59) participants (adjusted mean difference, −0.08 mL; 95% confidence interval, −0.30 to 0.15; P=0.50). Analyses suggested greater intervention effects with increasing baseline WMH volumes (P for interaction=0.03). New lacunar infarcts developed in 6 (9%) intervention and 2 (3%) control participants (odds ratio, 2.2; 95% confidence interval, 0.4–12.1; P=0.36). Conclusions— Nurse-led vascular care in hypertensive community-dwelling older persons did not diminish WMH accumulation over 3 years. However, our results do suggest this type of intervention could be effective in persons with high WMH volumes. There was no effect on lacunar infarcts incidence but numbers were low. Clinical Trial Information— URL: http://www.isrctn. com/ISRCTN29711771. Unique identifier: ISRCTN29711771.
Longitudinal connectome-based predictive modeling for REM sleep behavior disorder from structural brain connectivity

Methods to identify neuroplasticity patterns in human brains are of the utmost importance in understanding and potentially treating neurodegenerative diseases. Parkinson disease (PD) research will greatly benefit and advance from the discovery of biomarkers to quantify brain changes in the early stages of the disease, a prodromal period when subjects show no obvious clinical symptoms. Diffusion tensor imaging (DTI) allows for an in-vivo estimation of the structural connectome inside the brain and may serve to quantify the degenerative process before the appearance of clinical symptoms. In this work, we introduce a novel strategy to compute longitudinal structural connectomes in the context of a whole-brain data-driven pipeline. In these initial tests, we show that our predictive models are able to distinguish controls from asymptomatic subjects at high risk of developing PD (REM sleep behavior disorder, RBD) with an area under the receiving operating characteristic curve of 0.90 (p<0.001) and a longitudinal dataset of 46 subjects part of the Parkinson’s Progression Markers Initiative. By analyzing the brain connections most relevant for the predictive ability of the best performing model, we find connections that are biologically relevant to the disease.
Native Honey Bees Outperform Adventive Honey Bees in Increasing Pyrus bretschneideri (Rosales: Rosaceae) Pollination

Abstract The foraging behavior of different bee species is a key factor influencing the pollination efficiency of different crops. Most pear species exhibit full self-incompatibility and thus depend entirely on cross-pollination. However, as little is known about the pear visitation preferences of native Apis cerana (Fabricius; Hymenoptera: Apidae) and adventive Apis mellifera (L.; Hymenoptera: Apidae) in China. A comparative analysis was performed to explore the pear-foraging differences of these species under the natural conditions of pear growing areas. The results show significant variability in the pollen-gathering tendency of these honey bees. Compared to A. mellifera, A. cerana begins foraging at an earlier time of day and gathers a larger amount of pollen in the morning. Based on pollen collection data, A. mellifera shows variable preferences: vigorously foraging on pear on the first day of observation but collecting pollen from non-target floral resources on other experimental days. Conversely, A. cerana persists in pear pollen collection, without shifting preference to other competitive flowers. Therefore, A. cerana outperforms adventive A. mellifera with regard to pear pollen collection under natural conditions, which may lead to increased pear pollination. This study supports arguments in favor of further multiplication and maintenance of A. cerana for pear and other native crop pollination. Moreover, it is essential to develop alternative pollination management techniques to utilize A. mellifera for pear pollination.
[Factors Predicting the Interface Pressure Related to Pressure Injury in Intensive Care Unit Patients].

PURPOSE Interface pressure is a factor that contributes to the occurrence of pressure injuries. This study aimed to investigate interface pressure at common sites of pressure injury (occipital, gluteal and peritrochanteric areas), to explore the relationships among risk factors, skin condition and interface pressure, and to identify risk factors influencing interface pressure. METHODS A total of 100 patients admitted to the intensive care unit were enrolled at a tertiary teaching hospital in Korea. Interface pressure was recorded by a scanning aid device (PalmQ). Patient data regarding age, pulmonary disease, Braden Scale score, body mass index, serum albumin, hemoglobin, mean blood pressure, body temperature, and oxygen saturation were included as risk factors. Data collected from July to September 2016 were analyzed using binary logistic regression. RESULTS The mean interface pressure of the occipital, gluteal, and right and left peritrochanteric areas were 37.96 (±14.90), 41.15 (±16.04), 53.44 (±24.67), and 54.33 (±22.80) mmHg, respectively. Predictive factors for pressure injuries in the occipital area were age ≥70 years (OR 3.45, 95% confidence interval [CI]: 1.19~9.98), serum albumin deficit (OR 2.88, 95% CI: 1.00~8.26) and body temperature ≥36.5℃ (OR 3.12, 95% CI: 1.17~8.17); age ≥70 years (OR 2.81, 95% CI: 1.10~7.15) in the right peritrochanteric area; and body temperature ≥36.5℃ (OR 2.86, 95% CI: 1.17~6.98) in the left peritrochanteric area. CONCLUSION Our findings suggest that old age, hypoalbuminemia, and high body temperature may be contributory factors to increasing interface pressure; therefore, careful assessment and nursing care of these patients are needed to prevent pressure injury. Further studies are needed to establish cutoff values of interface pressure for patients with pressure ulcers.
The vacuole/lysosome is required for cell-cycle progression

Organelles are distributed to daughter cells, via inheritance pathways. However, it is unclear whether there are mechanisms beyond inheritance, which ensure that organelles are present in all cells. Here we present the unexpected finding that the yeast vacuole plays a positive essential role in initiation of the cell-cycle. When inheritance fails, a new vacuole is generated. We show that this occurs prior to the next cell-cycle, and gain insight into this alternative pathway. Moreover, we find that a combination of a defect in inheritance with an acute block in the vacuole biogenesis results in the loss of a functional vacuole and a specific arrest of cells in early G1 phase. Furthermore, this role for the vacuole in cell-cycle progression requires an intact TORC1-SCH9 pathway that can only signal from a mature vacuole. These mechanisms may serve as a checkpoint for the presence of the vacuole/lysosome. DOI: http://dx.doi. org/10.7554/eLife.08160. 001
Reef structure regulates small-scale spatial variation in coral bleaching

Coral bleaching is often characterized by high spatial variation across reef systems. Using a field survey and manipulative experiment, we tested whether the physical structure of coral reefs modifies environmental conditions that, in turn, influence spatial variation in bleaching in 3 scleractinian corals, Pocillopora verrucosa, Acropora elseyi, and Porites rus. Corals inhabit mainly the hard-bottom seafloor, or dead or partially dead coral heads ('bommies'). Bommies (0.10 to 3.0 m tall) position corals at different water depths and expose them to differences in light, temperature, hydrodynamics, and sedimentation, factors that can influence patterns of bleaching. We conducted our study in association with a 14 d warming event that caused bleaching in lagoons of Moorea, French Polynesia. Bleaching in naturally occurring colonies of Pocillopora spp. and Acopora spp. was greater on the seafloor (0 m tall) than on short (0.35 to 0.40 m tall) and tall bommies (1.0 to 1.2 m tall). Bleaching in P. verrucosa and A. elseyi transplanted to reef structures in the experiment generally decreased with increasing reef height (seafloor > short bommies > tall bommies). P. rus did not bleach under any conditions observed. Regression analyses revealed that reef structure controlled current speed and sedimentation at the microhabitat scale (from centimeters to meters), and that these factors regulated bleaching and mortality in P. verrucosa and A. elseyi. Our results imply that the physical structure of shallow water reef habitat influences the performance of coral colonies by modifying environmental stress, and that accounting for this structure is important in managing coral reef systems.
A new nearest neighbor classifier based on multi-harmonic mean distances

K-nearest neighbor (KNN) rule is a simple and effective classifier in pattern recognition. In this paper, we propose a new nearest neighbor classifier based on multi-harmonic mean distances, in order to overcome the sensitivity of the neighborhood size k and improve the classification performance. The proposed method is called a harmonic mean distance-based k-nearest neighbor classifier (HMDKNN). It mainly designs the multi-harmonic mean distances based on the multi-local mean vectors calculated by utilizing k nearest neighbors of the given query sample in each class. Using the multi-harmonic mean distances per class, a new nested harmonic mean distance in each class is designed as the classification decision and the query sample is classified into the class with the closest nested harmonic mean distance among all classes. The experimental results on the UCI data sets show that the proposed HMDKNN performs better with the less sensitiveness to k, compared to the state-of-art KNN-based methods.