Miracle-dz/UniFAR-FTUs huggingface dataset:
Expression of Root Genes in Arabidopsis Seedlings Grown by Standard and Improved Growing Methods

Roots of Arabidopsis thaliana seedlings grown in the laboratory using the traditional plant-growing culture system (TPG) were covered to maintain them in darkness. This new method is based on a dark chamber and is named the improved plant-growing method (IPG). We measured the light conditions in dark chambers, and found that the highest light intensity was dramatically reduced deeper in the dark chamber. In the bottom and side parts of dark chambers, roots were almost completely shaded. Using the high-throughput RNA sequencing method on the whole RNA extraction from roots, we compared the global gene expression levels in roots of seedlings from these two conditions and identified 141 differently expressed genes (DEGs) between them. According to the KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment, the flavone and flavonol biosynthesis and flavonoid biosynthesis pathways were most affected among all annotated pathways. Surprisingly, no genes of known plant photoreceptors were identified as DEGs by this method. Considering that the light intensity was decreased in the IPG system, we collected four sections (1.5 cm for each) of Arabidopsis roots grown in TPG and IPG conditions, and the spatial-related differential gene expression levels of plant photoreceptors and polar auxin transporters, including CRY1, CRY2, PHYA, PHYB, PHOT1, PHOT2, and UVR8 were analyzed by qRT-PCR. Using these results, we generated a map of the spatial-related expression patterns of these genes under IPG and TPG conditions. The expression levels of light-related genes in roots is highly sensitive to illumination and it provides a background reference for selecting an improved culture method for laboratory-maintained Arabidopsis seedlings.
Movement deficits and neuronal loss in basal ganglia in TRPC1 deficient mice

Transient receptor potential cation (TRPC) channel proteins are abundantly expressed in brain. However, the functions of these TRPC proteins such as TRPC1 are largely unclear. In this study, we reported that TRPC1 deficiency caused movement disorder as measured by swimming test, modified open field test and sunflower seeds eating test. Immunofluorescent staining showed significant loss of both NeuN-positive cells and tyrosine hydroxylase (TH) -positive cells in the caudate putamen (CPu), the external globus pallidus (GPe), and the substantia nigra pars reticulata (SNr) in 5-month-old TRPC1 knockout mice (TRPC1−/−) compared to the wild type (WT) mice. TUNEL staining further revealed that TUNEL-positive cells were significantly increased in the CPu, GPe, and SNr of TRPC1−/− mice. Taken together, these data suggests that TRPC1 is involved in the control of motor function by inhibiting the apoptosis of neuronal cells of basal ganglia.
Micromechanical Model for Heterogeneous Asphalt Concrete Mixtures Subjected to Fracture Failure

Cracking is a main source of structural distress in asphalt materials and asphaltic pavements. To predict crack-associated fracture damage in asphalt mixtures, this study presents a model using the finite-element method and a cohesive zone fracture model. The approach allows advanced characterization of the microstructural damage evolution in a more realistic length scale, the mixture heterogeneity, the inelastic material behavior, and the interactions among mixture constituents. The model presented herein accounts for (1) actual mixture heterogeneity by using digital image techniques; (2) inelastic material behavior based on elastic-viscoelastic constitutive relations; and (3) microscale fracture damage represented by the cohesive zone fracture model. A computational modeling framework is presented, and the applicability of the model is demonstrated through simulations. Model simulations are further analyzed by comparing numerical predictions to laboratory test results and by conducting parametric analyses of fracture properties. It is expected that the successfully developed computational model can provide better insights into the effect of mixture constituents on overall mixture performance, while minimizing modeling efforts and producing more accurate simulations than traditional approaches, with significant savings in experimental costs and time.
Coupled cascade regression for simultaneous facial landmark detection and head pose estimation

Current approaches for facial landmark detection and head pose estimation first perform landmark detection, followed by fitting 3D face model or regression model to estimate head pose. Different from the existing methods, in this paper, we propose a unified method, called Coupled Cascade Regression (CCR), for simultaneous facial landmark detection and head pose estimation. At each cascade level, two separate regressors are learned to update the landmark locations and 3D face model parameters based on the local appearance features, respectively. Since 2D facial landmark locations and head pose parameters are related, we further apply the projection model to refine the prediction results in each cascade iteration and make them consistent. As a result, CCR can leverage both the learning methods and the projection model to simultaneously perform facial landmark detection and pose estimation to enhance the performances of both tasks. Experimental results on 300-W and BU datasets indicate that our proposed CCR method outperforms many conventional methods both for landmark detection and head pose estimation.
3D Endoscopic Donor Nephrectomy Versus Robot-assisted Donor Nephrectomy: A Detailed Comparison of 2 Prospective Cohorts

Background There are 2 endoscopic surgical techniques that implement 3-dimensional (3D) vision to overcome visual misperception: 3D endoscopy and the da Vinci surgical system. 3D endoscopy has several advantages, such as the presence of tactile feedback and easy implementation, at lower costs. We aimed to assess whether 3D endoscopy could be an alternative to the robot during living donor nephrectomy. Methods Between April 2015 and April 2016, we prospectively collected data on 40 patients undergoing 3D endoscopic living donor nephrectomies in 1 center, performed by a da Vinci–certified surgeon. Data on donors’ perioperative results and recipient and graft survival were collected. These data were compared to 40 robot-assisted donor nephrectomies performed in the same center (between January 2012 and May 2014). Results Baseline characteristics for both groups were comparable. Intraoperative results showed a significantly shorter median skin-to-skin time of 138.5 minutes (125.8-163.8) versus 169.0 (141.5-209.8) minutes in favor of the 3D group (P = 0.001). Warm ischemia time (P = 0.003) and hilar phase for both single (1 artery and vein) and multiple anatomies (≥1 artery and/or vein [P = 0.002 and P = 0.010, respectively]) were also significantly reduced in favor of the 3D group, with a flat learning curve. Follow-up demonstrated no readmissions nor significant differences for donors, recipients, and graft survival. Conclusions 3D endoscopy may be a good alternative to robot-assisted donor nephrectomy because morbidity, graft, and recipient survival were comparable, with a significantly shorter median skin-to-skin time, warm ischemia time, and hilar dissection phase. Furthermore, implementation was easy and at lower costs, whereas tactile feedback was preserved.
Comments on 'A cone-beam filtered backprojection reconstruction algorithm for cardiac single photon emission computed tomography' by G. T. Gullberg and G. L. Zeng

In the above-titled work by G. T. Gullberg and G. L. Zeng (ibid., vol.11, no.1, p.91-101, 1992), a fan-beam reconstruction formula of a noncircular scanning locus was derived and extended for half-scan cone-beam reconstruction. However, the reconstruction formula is not exact mathematically unless a necessary condition is satisfied. In this correspondence, the commenters derive this necessary condition and provide a geometrical explanation of the condition.
On Use of Pulsed-Electrochemical Honing to Improve Micro-Geometry of Bevel Gears

Accuracy in micro-geometry is an important issue for gears because it affects noise generation and transmission characteristics and consequently determines the operating performance and service life of the gears. Various post-manufacturing processes are required to achieve the desired level of accuracy in micro-geometry of the gears. This paper reports on use of pulsed-electrochemical honing (PECH) process to improve micro-geometry of the straight bevel gears and presents experimental optimization of three important parameters of PECH namely pulse-on time, pulse-off time, and finishing time. Seventeen experiments were conducted according to central composite rotatable approach of response surface methodology. The improvements in micro-geometry of bevel gears in terms of average percentage improvement in single pitch error, adjacent pitch error, cumulative pitch error, and in total runout were found as 34.22%, 39.58%, 13.34%, and 18.88%, respectively. These improvements are better than those achieved using constant power supply due to efficient cleaning of the narrow inter-electrode gap during pulse-off time. These improvements lead to improve the gear quality up to seven for Deutsche Normen standard. Optimized values of input parameters for achieving these results are pulse-on time (2 ms), pulse-off time (4.5 ms), and finishing time (6 min).
Deploying Multiple Mobile Sinks in Event-Driven WSNs

Deploying multiple mobile sinks is an attractive approach to enhance the performance of wireless sensor networks. In this paper, we address the scenario of two mobile sinks. The two sinks can travel in the same region or in the divided regions separately. The problems are formulated by a lattice-based network model. We deduce the network lifetime and delay of data delivery in different mobility patterns. The relation between network performance and number of mobile sinks is also discussed. Simulation results are provided to validate our theoretic analysis followed by performance comparison of different mobility patterns.
ATM and p53 combined analysis predicts survival in glioblastoma multiforme patients: A clinicopathologic study

Glioblastoma is one of the most malignant cancers, with a distinguishing dismal prognosis: surgery followed by chemo‐ and radiotherapy represents the current standard of care, and chemo‐ and radioresistance underlie disease recurrence and short overall survival of patients suffering from this malignancy. ATM is a kinase activated by autophosphorylation upon DNA doublestrand breaks arising from errors during replication, byproducts of metabolism, chemotherapy or ionizing radiations; TP53 is one of the most popular tumor suppressor, with a preeminent role in DNA damage response and repair. To study the effects of the immunohistochemical expression of p‐ATM and p53 in glioblastoma patients, 21 cases were retrospectively examined. In normal brain tissue, p‐ATM was expressed only in neurons; conversely, in tumors cells, the protein showed a variable cytoplasmic expression (score: +,++,+++), with being completely undetectable in three cases. Statistical analysis revealed that high p‐ATM score (++/+++) strongly correlated to shorter survival (P = 0.022). No difference in overall survival was registered between p53 normally expressed (NE) and overexpressed (OE) glioblastoma patients (P = 0.669). Survival analysis performed on the results from combined assessment of the two proteins showed that patients with NE p53 /low pATM score had longer overall survival than the NE p53/ high pATM score counterpart. Cox‐regression analysis confirmed this finding (HR = 0.025; CI 95% = 0.002–0.284; P = 0.003). Our study outlined the immunohistochemical expression of p‐ATM/p53 in glioblastomas and provided data on their possible prognostic/predictive of response role. A “non‐oncogene addiction” to ATM for NEp53 glioblastoma could be postulated, strengthening the rationale for development of ATM inhibiting drugs.
Age-specific associations of reduced estimated glomerular filtration rate with concurrent chronic kidney disease complications.

BACKGROUND AND OBJECTIVES It has been suggested that moderate reductions in estimated GFR (eGFR) among older adults may not reflect chronic kidney disease (CKD). DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS We examined age-specific (<60, 60 to 69, 70 to 79, and ≥80 years) associations between eGFR level and six concurrent CKD complications among 30,528 participants from the National Health and Nutrition Examination Survey (NHANES) 1988 to 1994 and 1999 to 2006 (n = 8242 from NHANES 2003 to 2006 for hyperparathyroidism). Complications included anemia (hemoglobin <12 g/dl women, <13.5 g/dl men), acidosis (bicarbonate <22 mEq/L), hyperphosphatemia (phosphorus ≥4.5 mg/dl), hypoalbuminemia (albumin <3.5 mg/dl), hyperparathyroidism (intact parathyroid hormone ≥70 pg/ml), and hypertension (systolic/diastolic BP ≥140/90 mmHg or antihypertensive use). RESULTS Among participants ≥80 years old, compared with those with estimated GFR (eGFR) ≥60 ml/min per 1.73 m(2), the multivariable adjusted prevalence ratios (95% confidence interval) associated with eGFR levels of 45 to 59 and <45 ml/min per 1.73 m(2) were 1.39 (1.11 to1.73) and 2.06 (1.59 to 2.67) for anemia, 1.33 (0.89 to 1.98) and 2.47 (1.52 to 4.00) for acidosis, 1.11 (0.70 to 1.76) and 2.16 (1.36 to 3.42) for hyperphosphatemia, 2.04 (1.39 to 3.00) and 2.83 (1.76 to 4.53) for hyperparathyroidism and 1.09 (1.03 to 1.14), and 1.12 (1.05 to 1.19) for hypertension, respectively. Higher prevalence ratios for these complications at lower eGFR levels were also present at younger ages. Reduced eGFR was associated with hypoalbuminemia only for adults <70. CONCLUSIONS Reduced eGFR was associated with a higher prevalence of several concurrent CKD complications, regardless of age.
Outlier Detection for Sensor Systems (ODSS): A MATLAB Macro for Evaluating Microphone Sensor Data Quality

Microphone sensor systems provide information that may be used for a variety of applications. Such systems generate large amounts of data. One concern is with microphone failure and unusual values that may be generated as part of the information collection process. This paper describes methods and a MATLAB graphical interface that provides rapid evaluation of microphone performance and identifies irregularities. The approach and interface are described. An application to a microphone array used in a wind tunnel is used to illustrate the methodology.
A single N‐terminal phosphomimic disrupts TDP‐43 polymerization, phase separation, and RNA splicing

TDP‐43 is an RNA‐binding protein active in splicing that concentrates into membraneless ribonucleoprotein granules and forms aggregates in amyotrophic lateral sclerosis (ALS) and Alzheimer's disease. Although best known for its predominantly disordered C‐terminal domain which mediates ALS inclusions, TDP‐43 has a globular N‐terminal domain (NTD). Here, we show that TDP‐43 NTD assembles into head‐to‐tail linear chains and that phosphomimetic substitution at S48 disrupts TDP‐43 polymeric assembly, discourages liquid–liquid phase separation (LLPS) in vitro, fluidizes liquid–liquid phase separated nuclear TDP‐43 reporter constructs in cells, and disrupts RNA splicing activity. Finally, we present the solution NMR structure of a head‐to‐tail NTD dimer comprised of two engineered variants that allow saturation of the native polymerization interface while disrupting higher‐order polymerization. These data provide structural detail for the established mechanistic role of the well‐folded TDP‐43 NTD in splicing and link this function to LLPS. In addition, the fusion‐tag solubilized, recombinant form of TDP‐43 full‐length protein developed here will enable future phase separation and in vitro biochemical assays on TDP‐43 function and interactions that have been hampered in the past by TDP‐43 aggregation.
Association Between Achieved Low-Density Lipoprotein Levels and Major Adverse Cardiac Events in Patients With Stable Ischemic Heart Disease Taking Statin Treatment.

IMPORTANCE International guidelines recommend treatment with statins for patients with preexisting ischemic heart disease to prevent additional cardiovascular events but differ regarding target levels of low-density lipoprotein cholesterol (LDL-C). Trial data on this question are inconclusive and observational data are lacking. OBJECTIVE To assess the relationship between levels of LDL-C achieved with statin treatment and cardiovascular events in adherent patients with preexisting ischemic heart disease. DESIGN, SETTING, AND PARTICIPANTS Population-based observational cohort study from 2009 to 2013 using data from a health care organization in Israel covering more than 4.3 million members. Included patients had ischemic heart disease, were aged 30 to 84 years, were treated with statins, and were at least 80% adherent to treatment or, in a sensitivity analysis, at least 50% adherent. Patients with active cancer or metabolic abnormalities were excluded. EXPOSURES Index LDL-C was defined as the first achieved serum LDL-C measure after at least 1 year of statin treatment, grouped as low (≤70.0 mg/dL), moderate (70.1-100.0 mg/dL), or high (100.1-130.0 mg/dL). MAIN OUTCOMES AND MEASURES Major adverse cardiac events included acute myocardial infarction, unstable angina, stroke, angioplasty, bypass surgery, or all-cause mortality. The hazard ratio of adverse outcomes was estimated using 2 Cox proportional hazards models with low vs moderate and moderate vs high LDL-C, adjusted for confounders and further tested using propensity score matching analysis. RESULTS The cohort with at least 80% adherence included 31 619 patients, for whom the mean (SD) age was 67.3 (9.8) years. Of this population, 27% were female and 29% had low, 53% moderate, and 18% high LDL-C when taking statin treatment. Overall, there were 9035 patients who had an adverse outcome during a mean 1.6 years of follow-up (6.7 per 1000 persons per year). The adjusted incidence of adverse outcomes was not different between low and moderate LDL-C (hazard ratio [HR], 1.02; 95% CI, 0.97-1.07; P = .54), but it was lower with moderate vs high LDL-C (HR, 0.89; 95% CI, 0.84-0.94; P < .001). Among 54 884 patients with at least 50% statin adherence, the adjusted HR was 1.06 (95% CI, 1.02-1.10; P = .001) in the low vs moderate groups and 0.87 (95% CI, 0.84-0.91; P = .001) in the moderate vs high groups. CONCLUSIONS AND RELEVANCE Patients with LDL-C levels of 70 to 100 mg/dL taking statins had lower risk of adverse cardiac outcomes compared with those with LDL-C levels between 100 and 130 mg/dL, but no additional benefit was gained by achieving LDL-C of 70 mg/dL or less. These population-based data do not support treatment guidelines recommending very low target LDL-C levels for all patients with preexisting heart disease.
Medium-term effects of dietary nitrate supplementation on systolic and diastolic blood pressure in adults: a systematic review and meta-analysis

Objectives: Dietary nitrate supplementation has been shown to lower blood pressure (BP) particularly in short-term clinical trials. Whether these effects are sustained in the long-term remains to be established. The objective was to conduct a meta-analysis of randomized controlled trials that examined whether dietary nitrate supplementation for more than 1 week has beneficial effects on SBP and DBP. Methods: Electronic databases were searched from inception until May 2016. Specific inclusion criteria were duration at least 1 week, report of effects on SBP or DBP or both and comparison of inorganic nitrate or beetroot juice supplementation with placebo control groups. Random-effects models were used to calculate the pooled BP effect sizes. Results: Thirteen trials met eligibility criteria. The trials included a total of 325 participants with seven to 65 participants per study. The duration of each intervention ranged from 1 to 6 weeks. Ten trials assessed BP in resting clinic conditions, whereas 24-h ambulatory and daily home monitorings were used in six and three trials, respectively. Overall, dietary nitrate was associated with a significant decline in SBP [−4.1 mmHg (95% confidence interval: −6.1, −2.2); P < 0.001] and DBP [−2.0 mmHg (95% confidence interval: −3.0, −0.9); P < 0.001]. However, the effect was only significant when measured in resting clinical settings as no significant changes in BP were observed using 24-h ambulatory and daily home BP monitorings. Conclusion: Positive effects of medium-term dietary nitrate supplementation on BP were only observed in clinical settings, which were not corroborated by more accurate methods such as 24-h ambulatory and daily home monitorings.
Randomised controlled trial of long-term maintenance corticosteroid therapy in patients with autoimmune pancreatitis

Objective Corticosteroid has been established as the standard therapy for autoimmune pancreatitis (AIP), but the requirement for maintenance corticosteroid therapy is controversial. We conducted a randomised controlled trial to clarify the efficacy of maintenance corticosteroid therapy in patients with AIP. Design We conducted a multicentre, tertiary setting, randomised controlled trial. After the induction of remission with the initial oral prednisolone (PSL) treatment, maintenance therapy with PSL at 5–7.5 mg/day was continued for 3 years or withdrawn at 26 weeks. The primary endpoint was relapse-free survival over 3 years and the secondary endpoint was serious corticosteroid-related complications. All analyses were performed on an intention-to-treat basis. Results Between April 2009 and March 2012, 49 patients with AIP were randomly assigned to the maintenance therapy group (n=30) or the cessation group (n=19). Baseline characteristics were not different between the two groups. Relapses occurred within 3 years in 11 out of 19 (57.9%) patients assigned to the cessation group, and in 7 of 30 (23.3%) patients in the maintenance therapy group. The relapse rate over 3 years was significantly lower in the maintenance therapy group than that in the cessation group (p=0.011). The relapse-free survival was significantly longer in the maintenance therapy group than that in the cessation group (p=0.007). No serious corticosteroid-related complications requiring discontinuation of PSL were observed. Conclusions Maintenance corticosteroid therapy for 3 years may decrease relapses in patients with AIP compared with those who discontinued the therapy at 26 weeks. Trial registration number UMIN000001818; Results.
Selecting of FBG Coatings for Quench Detection in HTS Coils

Fiber Bragg grating (FBG) temperature sensors are now regarded as a relatively mature sensing technology for temperature measurement in ambient conditions, and may offer potential as a cryogenic temperature sensor for quench detection. In this paper, the temperature response of three different coated FBG sensors from 77 to 293 K was studied; bare (silica) FBG, acrylic coated, and polyimide coated FBG sensors. We examine the effect of fiber coatings on the temperature sensitivity of an embedded FBG sensor down to cryogenic temperatures. Measurements were repeated with sensors from two FBG suppliers. The measured temperature response was then compared and contrasted with the predicted sensor response. In order to assess the sensor sensitivity, repeatability, and any hysteresis, these sensors were then subjected to repeated cool-down / warm-up cycles (77–293 K). The effect of epoxy resin impregnation on the temperature response characteristics was analyzed by comparing the sensor response characteristics before and after embedding into a 10 mm × 2 mm × 4 mm epoxy block. We compare this to the uncoated fiber for embedment in HTS coils. Finally, we recommend the optimum low-cost sensor construction for use in quench detection in coils.