Miracle-dz/UniFAR-FTUs huggingface dataset:
The planar cell polarity gene strabismus regulates convergence and extension and neural fold closure in Xenopus.

We cloned Xenopus Strabismus (Xstbm), a homologue of the Drosophila planar cell or tissue polarity gene. Xstbm encodes four transmembrane domains in its N-terminal half and a PDZ-binding motif in its C-terminal region, a structure similar to Drosophila and mouse homologues. Xstbm is expressed strongly in the deep cells of the anterior neural plate and at lower levels in the posterior notochordal and neural regions during convergent extension. Overexpression of Xstbm inhibits convergent extension of mesodermal and neural tissues, as well as neural tube closure, without direct effects on tissue differentiation. Expression of Xstbm(DeltaPDZ-B), which lacks the PDZ-binding region of Xstbm, inhibits convergent extension when expressed alone but rescues the effect of overexpressing Xstbm, suggesting that Xstbm(DeltaPDZ-B) acts as a dominant negative and that both increase and decrease of Xstbm function from an optimum retards convergence and extension. Recordings show that cells expressing Xstbm or Xstbm(DeltaPDZ-B) fail to acquire the polarized protrusive activity underlying normal cell intercalation during convergent extension of both mesodermal and neural and that this effect is population size-dependent. These results further characterize the role of Xstbm in regulating the cell polarity driving convergence and extension in Xenopus.
Effects of Achillea wilhelmsii on rat’s gastric acid output at basal, vagotomized, and vagal-stimulated conditions

Background: Achillea is a plant widely used in traditional medicine for gastrointestinal disorders. There are some reports on gastrointestinal effects of Achillea, such as antiulcer, antibacterial, hepatoprotective, choleretic, and antispasmodic. To investigate the effects of aqueous–ethanol extract of Achillea wilhelmsii on rat’s gastric acid output in basal, vagotomized (VX), and vagal-stimulated conditions. Materials and Methods: 24 male Wistar rats were randomly divided into 2 groups: control and test. Gastroduodenostomy was performed for each rat. Gastric content was collected for 30 min by washout technique. One milliliter of 3 doses (0.5, 1, and 2 mg/kg) was introduced into the stomach of each rat in the test group and the same volume of saline was used in the control group. Total titratable acid was measured by a titrator. Results: The extract inhibited acid output significantly in basal condition by 1 and 2 mg/kg doses (P < 0.05) but in VX condition this inhibitory effect on acid output disappeared and the 1 and 2 mg/kg doses increased acid output significantly (P < 0.05 and P < 0.001, respectively). The extract showed a reduction in the acid output in vagal-stimulated condition by 1 and 2 mg/kg doses, which were not statistically significant. Conclusion: These results showed an inhibitory effect of A. wilhelmsii extract on acid output in basal condition. The inhibitory effect of the extract was exerted via gastric vagal parasympathetic nerve.
On the parameterized complexity of approximating dominating set

We study the parameterized complexity of approximating the k-Dominating Set (domset) problem where an integer k and a graph G on n vertices are given as input, and the goal is to find a dominating set of size at most F(k) · k whenever the graph G has a dominating set of size k. When such an algorithm runs in time T(k)poly(n) (i.e., FPT-time) for some computable function T, it is said to be an F(k)-FPT-approximation algorithm for k-domset. Whether such an algorithm exists is listed in the seminal book of Downey and Fellows (2013) as one of the ”most infamous” open problems in Parameterized Complexity. This work gives an almost complete answer to this question by showing the non-existence of such an algorithm under W[1]≠FPT and further providing tighter running time lower bounds under stronger hypotheses. Specifically, we prove the following for every computable functions T, F and every constant ε > 0: (i) Assuming W[1]≠FPT, there is no F(k)-FPT-approximation algorithm for k-domset, (ii) Assuming the Exponential Time Hypothesis (ETH), there is no F(k)-approximation algorithm for k-domset that runs in T(k)no(k) time, (iii) Assuming the Strong Exponential Time Hypothesis (SETH), for every integer k ≥ 2, there is no F(k)-approximation algorithm for k-domset that runs in T(k)nk − ε time, (iv) Assuming the k-sum Hypothesis, for every integer k ≥ 3, there is no F(k)-approximation algorithm for k-domset that runs in T(k) n⌈ k/2 ⌉ − ε time. Previously, only constant ratio FPT-approximation algorithms were ruled out under W[1]≠FPT and (log1/4 − ε k)-FPT-approximation algorithms were ruled out under ETH [Chen and Lin, FOCS 2016]. Recently, the non-existence of an F(k)-FPT-approximation algorithm for any function F was shown under gapETH [Chalermsook et al., FOCS 2017]. Note that, to the best of our knowledge, no running time lower bound of the form nδ k for any absolute constant δ > 0 was known before even for any constant factor inapproximation ratio. Our results are obtained by establishing a connection between communication complexity and hardness of approximation, generalizing the ideas from a recent breakthrough work of Abboud et al. [FOCS 2017]. Specifically, we show that to prove hardness of approximation of a certain parameterized variant of the label cover problem, it suffices to devise a specific protocol for a communication problem that depends on which hypothesis we rely on. Each of these communication problems turns out to be either a well studied problem or a variant of one; this allows us to easily apply known techniques to solve them.
Modeling of Electroporation Induced by Pulsed Electric Fields in Irregularly Shaped Cells

During the past decades, the poration of cell membrane induced by pulsed electric fields has been widely investigated. Since the basic mechanisms of this process have not yet been fully clarified, many research activities are focused on the development of suitable theoretical and numerical models. To this end, a nonlinear, nonlocal, dispersive, and space-time numerical algorithm has been developed and adopted to evaluate the transmembrane voltage and pore density along the perimeter of realistic irregularly shaped cells. The presented model is based on the Maxwell's equations and the asymptotic Smoluchowski's equation describing the pore dynamics. The dielectric dispersion of the media forming the cell has been modeled by using a general multirelaxation Debye-based formulation. The irregular shape of the cell is described by using the Gielis’ superformula. Different test cases pertaining to red blood cells, muscular cells, cell in mitosis phase, and cancer-like cell have been investigated. For each type of cell, the influence of the relevant shape, the dielectric properties, and the external electric pulse characteristics on the electroporation process has been analyzed. The numerical results demonstrate that the proposed model is an efficient numerical tool to study the electroporation problem in arbitrary-shaped cells.
Outage analysis for path selection based MIMO-beamforming cooperative wireless systems with node mobility and imperfect CSI

This paper presents an analysis for the end-to-end SNR outage probability of a multiple-input multiple-output (MIMO) beamforming based cooperative wireless communication system considering the effects of node mobility and channel estimation errors. Closed form expressions are derived for the per-block SNR outage probability as well as the asymptotic outage floor. Simulation results illustrate the outage performance of the MIMO beamforming based DF cooperative path selection scheme under various node mobility scenarios and verify the analytical results derived. Interestingly, it is observed that except for scenarios in which only the relay node is mobile with static source and destination nodes, the system always experiences an asymptotic error floor with SNR due to node mobility.
Remarkable heterogeneity in meso‐ and bathypelagic bacterioplankton assemblage composition

We investigated meso‐ to bathypelagic (500‐3,000 m) bacterioplankton assemblage composition at 19 locations in the North Atlantic Ocean beneath the offshore Amazon River plume, in the North Pacific Ocean near the Hawaiian archipelago, at the San Pedro Ocean Time Series (SPOTS) station off southern California, and in the Coral Sea off eastern Australia with a sensitive high‐throughput fingerprinting approach, automated rRNA intergenic spacer analysis (ARISA), to examine variation between bacterial assemblages at different stations. Temperature and salinity were used to identify distinct water masses within gyres. ARISA fingerprints each contained 15‐117 operational taxonomic units (OTUs) per assemblage; however, the OTU composition of fingerprints varied among stations, even within the same water mass. Fingerprints from 500 m at the SPOTS station over 4 yr shared on average a Sorensen Index (proportional representation similarity) of 0.68 ± 0.01, whereas at more oceanic stations at 500 m, fingerprints shared a Sorensen Index of 0.48 ± 0.01 and a Whittaker Index of 0.38 ± 0.01. At deeper depths (1,000 and 2,000 m), fingerprints were equally variable, sharing Sorensen Indices of 0.42 ± 0.02 and 0.50 ± 0.02 and Whittaker indices of 0.33 ± 0.01 and 0.34 ± 0.03, at 1,000 m and 3,000 m, respectively. Mesopelagic, moderately productive waters were more stable than those at less productive, open‐ocean gyre stations, suggesting that variability in bacterioplankton communities at depth is influenced by organic matter supply and patchiness.
Variance of the Parental Genome Contribution to Inbred Lines Derived From Biparental Crosses

The expectation of the parental genome contribution to inbred lines derived from biparental crosses or backcrosses is well known, but no theoretical results exist for its variance. Our objective was to derive the variance of the parental genome contribution to inbred lines developed by the single-seed descent or double haploid method from biparental crosses or backcrosses. We derived formulas and tabulated results for the variance of the parental genome contribution depending on the chromosome lengths and the mating scheme used for inbred line development. A normal approximation of the probability distribution function of the parental genome contribution fitted well the exact distribution obtained from computer simulations. We determined upper and lower quantiles of the parental genome contribution for model genomes of sugar beet, maize, and wheat using normal approximations. These can be employed to detect essentially derived varieties in the context of plant variety protection. Furthermore, we outlined the application of our results to predict the response to selection. Our results on the variance of the parental genome contribution can assist breeders and geneticists in the design of experiments or breeding programs by assessing the variation around the mean parental genome contribution for alternative crossing schemes.
Enhanced Electrostatic Integrity of Short-Channel Junctionless Transistor With High- $\kappa$ Spacers

We propose the use of a high-κ spacer to improve the electrostatic integrity and, thereby, the scalability of silicon junctionless transistors (JLTs) for the first time. Using extensive simulations of n-channel JLTs, we demonstrate that the high-κ spacers improve the electrostatic integrity of JLTs at sub-22-nm gate lengths. Electric field that fringes through the high-κ spacer to the device layer on either sides of the gate results in an effective increase in electrical gate length in the off-state. However, the effective gate length is unaffected in the on-state. Hence, the off-state leakage current is reduced by several orders of magnitude with the use of a high-κ spacer with concomitent improvements in the subthreshold swing and drain-induced barrier lowering. A marginal improvement in the on-state current is observed with the use of the high-κ spacer, and this is related to the reduction in parasitic resistance in the silicon under the spacer due to fringe fields.
Real Time ELA De-Interlacing with the Xtensa Reconfigurable Processor

This paper proposes optimization techniques to accelerate the enhanced edge-based line average (ELA) de-interlacing method. ELA is based on edge detection and directional interpolation as well as median filtering. The techniques are first based on low-level software optimizations to accelerate loops and arithmetic operations. Specialized hardware structures and corresponding new instructions are then defined for the Xtensa reconfigurable processor to accelerate ELA-specific operations. The combined software and hardware techniques result in a speed-up of 67x when compared to a base case. This accelerates the processing time from 25 times slower than real time to 2.7 times faster for a NTSC frame rate. A parallel processing version of ELA is also discussed
Multidisciplinary approaches to understanding collective cell migration in developmental biology

Mathematical models are becoming increasingly integrated with experimental efforts in the study of biological systems. Collective cell migration in developmental biology is a particularly fruitful application area for the development of theoretical models to predict the behaviour of complex multicellular systems with many interacting parts. In this context, mathematical models provide a tool to assess the consistency of experimental observations with testable mechanistic hypotheses. In this review, we showcase examples from recent years of multidisciplinary investigations of neural crest cell migration. The neural crest model system has been used to study how collective migration of cell populations is shaped by cell–cell interactions, cell–environmental interactions and heterogeneity between cells. The wide range of emergent behaviours exhibited by neural crest cells in different embryonal locations and in different organisms helps us chart out the spectrum of collective cell migration. At the same time, this diversity in migratory characteristics highlights the need to reconcile or unify the array of currently hypothesized mechanisms through the next generation of experimental data and generalized theoretical descriptions.
Incidence of ischemic stroke in Japanese patients with atrial fibrillation not receiving anticoagulation therapy--pooled analysis of the Shinken Database, J-RHYTHM Registry, and Fushimi AF Registry.

BACKGROUND The incidence rate of ischemic stroke in Japanese non-valvular atrial fibrillation (NVAF) patients without anticoagulation therapy remains unclear. METHODS AND RESULTS We performed a pooled analysis of 3,588 patients from the Shinken Database (n=1,099), J-RHYTHM Registry (n=1,002), and Fushimi AF Registry (n=1,487) to determine the incidence rate of ischemic stroke in Japanese NVAF patients without anticoagulation therapy. Average patient age was 68.1 years. During the follow-up period (total, 5,188 person-years; average, 1.4 years), 69 patients suffered from ischemic stroke (13.3 per 1,000 person-years; 95% confidence intervals [CI]: 10.5-16.8). The incidence rates of ischemic stroke were 5.4, 9.3, and 24.7 per 1,000 person-years and 5.3, 5.5, and 18.4 per 1,000 person-years in patients with low (0), intermediate (1), and high (≥ 2) CHADS2 and CHA2DS2-VASc scores, respectively. History of ischemic stroke or transient ischemic attack (hazard ratio [HR], 3.25; 95% CI: 1.86-5.67), age ≥ 75 years (HR, 2.31; 95% CI: 1.18-4.52), and hypertension (HR, 1.69; 95% CI: 1.01-2.86) were independent risk factors for ischemic stroke. CONCLUSIONS A low incidence rate of ischemic stroke was observed in Japanese NVAF patients except for those with CHADS2 score ≥ 2. In this pooled analysis, history of ischemic stroke or transient ischemic attack, advanced age, and hypertension were identified as independent risk factors for ischemic stroke.
EVALUATİON OF EFFECTS OF S-METHYL ISOTHİOUREA AND MELATONİN ON INTESTİNAL ISCHEMİA/REPERFUSİON INJURY IN RATS

The present study was designed to evaluate whether the administration of s-methylisothiourea and melatonin has protective potential in intestinal ischemia/reperfusion injury. Forty male Sprague-Dawley rats were divided into five groups. Ileal specimens were obtained to determine the levels of malondialdehyde, protein carbonyl content, levels of antioxidant enzymes and evaluation of histologic changes. Combination of s-methylisothiourea and melatonin, led to a statistically significant increase in activities of antioxidant enzymes with a decrease in malondialdehyde and protein carbonyl content and intestinal mucosal injury scores. It was shown; combination of SMT and melatonin may exert more promised results.
L1-Mediated Branching Is Regulated by Two Ezrin-Radixin-Moesin (ERM)-Binding Sites, the RSLE Region and a Novel Juxtamembrane ERM-Binding Region

We investigated how the neural cell adhesion molecule L1 mediates neurite outgrowth through L1-L1 homophilic interactions. Wild-type L1 and L1 with mutations in the cytoplasmic domain (CD) were introduced into L1 knock-out neurons, and transfected neurons were grown on an L1 substrate. Neurite length and branching were compared between wild-type L1 and L1CD mutations. Surprisingly, the L1CD is not required for L1-mediated neurite outgrowth but plays a critical role in neurite branching, through both the juxtamembrane region and the RSLE region. We demonstrate that both regions serve as ezrin-moesin-radixin-binding sites. A truncation mutant that deletes 110 of 114 amino acids of the L1CD still supports neurite outgrowth on an L1 substrate, suggesting that a coreceptor binds to L1 in cis and mediates neurite outgrowth and that L1-ankyrin interactions are not essential for neurite initiation or outgrowth. These data are consistent with a model in which L1 can influence L1-mediated neurite outgrowth and branching through both the L1CD and a coreceptor.
Fibroblast mitogenic activity of lung lavage fluid from infants with chronic lung disease of prematurity

Background: Lung fibrosis is thought to be important in chronic lung disease of prematurity (CLD). Methods: Fibroblast proliferative activity was assessed in 207 bronchoalveolar lavage fluid (BALF) samples from 43 infants. Sixteen developed CLD (birth weight 765 g (630–1230), gestation 26.5 weeks (23–29)), 18 developed respiratory distress syndrome (RDS) (birth weight 1415 g (430–4160), gestation 31 weeks (23–39)), and nine control infants (birth weight 2110 g (900–3720), gestation 32 weeks (26–41)) received mechanical ventilation for non-pulmonary reasons. Results: The fibroblast proliferative activity relative to 10% fetal calf serum was 64–75% in infants with CLD, 55–86% in the RDS group, and 42–68% in control infants during the first 5 weeks of life. Only at day 3 was there a difference between the groups (CLD 72% v control 42%, p < 0.01; RDS 63% v control 42%, p < 0.05). With the use of neutralising antibodies, platelet derived growth factor BB (PDGF-BB) and epidermal growth factor were undetectable, and insulin-like growth factor I (IGF-I) accounted for 14% (p < 0.05) and 11% (p < 0.005) of BALF mitogenic activity from the RDS and CLD groups respectively. Conclusions: The mitogenic activity of BALF was similar in the three groups studied and was only partially accounted for by IGF-I. Growth factors other than PDGF-BB and IGF-I contribute significantly to this process.
Increasing Dengue Incidence in Singapore over the Past 40 Years: Population Growth, Climate and Mobility

In Singapore, the frequency and magnitude of dengue epidemics have increased significantly over the past 40 years. It is important to understand the main drivers for the rapid increase in dengue incidence. We studied the relative contributions of putative drivers for the rise of dengue in Singapore: population growth, climate parameters and international air passenger arrivals from dengue endemic countries, for the time period of 1974 until 2011. We used multivariable Poisson regression models with the following predictors: Annual Population Size; Aedes Premises Index; Mean Annual Temperature; Minimum and Maximum Temperature Recorded in each year; Annual Precipitation and Annual Number of Air Passengers arriving from dengue-endemic South-East Asia to Singapore. The relative risk (RR) of the increase in dengue incidence due to population growth over the study period was 42.7, while the climate variables (mean and minimum temperature) together explained an RR of 7.1 (RR defined as risk at the end of the time period relative to the beginning and goodness of fit associated with the model leading to these estimates assessed by pseudo-R2 equal to 0.83). Estimating the extent of the contribution of these individual factors on the increasing dengue incidence, we found that population growth contributed to 86% while the residual 14% was explained by increase in temperature. We found no correlation with incoming air passenger arrivals into Singapore from dengue endemic countries. Our findings have significant implications for predicting future trends of the dengue epidemics given the rapid urbanization with population growth in many dengue endemic countries. It is time for policy-makers and the scientific community alike to pay more attention to the negative impact of urbanization and urban climate on diseases such as dengue.
Adriamycin increases podocyte permeability: evidence and molecular mechanism.

OBJECTIVE To investigate the increased podocyte permeability by evidence of adriamycin (AD) and its molecular mechanism. METHODS In this study, we explored the direct effects of AD on cultured mouse podocytes and the potential protection effects of Dexamethasome (Dex). RESULTS After 24-hour AD (5 x 10(-7) mol/L) treatment, albumin passage through podocyte monolayers was increased by 2.27-fold (P < 0.01). AD caused a 62% decrease in Zonula Occluden-1 (ZO-1) protein (P < 0.05), suggesting that AD might increase podocyte permeability by disrupting tight junctions. Dex (1 x 10(-6) mol/L), co-administered with AD, protected podocytes from AD-induced increased albumin passage. This may be linked with an increased P-cadherin protein level to 1.93 fold of control (P < 0.01). CONCLUSIONS AD has a direct, detrimental effect on podocyte permeability, probably through disrupting tight junctions; Dex could protect against AD-induced high podocyte permeability by upregulating adherent protein P-cadherin.
Modeling the behavior of fiber reinforced polymer-confined concrete columns exposed to fire

Very little information is available on the behavior of fiber reinforced polymer (FRP) materials and FRP-strengthened concrete members in fire, and this is a primary factor hindering the widespread implementation of FRP strengthening technologies in the construction industry. This paper presents a numerical model for evaluating the fire behavior of conventionally reinforced circular concrete columns, FRP-wrapped reinforced concrete columns, and insulated FRP-wrapped reinforced concrete columns. The model is validated against data available in the literature from full-scale fire endurance tests on conventionally reinforced concrete columns, and preliminary predictions of the model are presented and discussed. It is demonstrated that the model agrees reasonably well with experimental data obtained from tests on circular reinforced concrete columns, that it is unlikely that the structural effectiveness of FRP materials can be maintained during fire, and that the fire behavior of FRP-wrapped columns can be dramatically improved by providing supplemental insulation for the FRP.