Miracle-dz/UniFAR-FTUs huggingface dataset:
Genome-wide survey and comprehensive expression profiling of Aux/IAA gene family in chickpea and soybean

Auxin plays a central role in many aspects of plant growth and development. Auxin/Indole-3-Acetic Acid (Aux/IAA) genes cooperate with several other components in the perception and signaling of plant hormone auxin. An investigation of chickpea and soybean genomes revealed 22 and 63 putative Aux/IAA genes, respectively. These genes were classified into six subfamilies on the basis of phylogenetic analysis. Among 63 soybean Aux/IAA genes, 57 (90.5%) were found to be duplicated via whole genome duplication (WGD)/segmental events. Transposed duplication played a significant role in tandem arrangements between the members of different subfamilies. Analysis of Ka/Ks ratio of duplicated Aux/IAA genes revealed purifying selection pressure with restricted functional divergence. Promoter sequence analysis revealed several cis-regulatory elements related to auxin, abscisic acid, desiccation, salt, seed, and endosperm, indicating their role in development and stress responses. Expression analysis of chickpea and soybean Aux/IAA genes in various tissues and stages of development demonstrated tissue/stage specific differential expression. In soybean, at least 16 paralog pairs, duplicated via WGD/segmental events, showed almost indistinguishable expression pattern, but eight pairs exhibited significantly diverse expression patterns. Under abiotic stress conditions, such as desiccation, salinity and/or cold, many Aux/IAA genes of chickpea and soybean revealed differential expression. qRT-PCR analysis confirmed the differential expression patterns of selected Aux/IAA genes in chickpea. The analyses presented here provide insights on putative roles of chickpea and soybean Aux/IAA genes and will facilitate elucidation of their precise functions during development and abiotic stress responses.
HtrA1: Its future potential as a novel biomarker for cancer

HtrA1 appears to be involved in several physiological processes as well as in the pathogenesis of conditions such as Alzheimer’s disease and osteoarthritis. It has also been hypothesized to play a role as a tumor suppressor. This manuscript reviews the current cancer-related HtrA1 research from the methodological and clinical standpoints including studies regarding its potential role as a tumor marker and/or prognostic factor. PRISMA method was used for study selection. The articles thus collected were examined and selected by two independent reviewers; any disagreement was resolved by a methodologist. A laboratory researcher reviewed the methods and laboratory techniques. Fifteen studies met the inclusion criteria and concerned the following cancer sites: the nervous system, bladder, breast, esophagus, stomach, liver, endometrium, thyroid, ovaries, pleura, lung and skin. Most articles described in vivo studies using a morphological approach and immunohistochemistry, whereas protein expression was quantified as staining intensity scored by two raters. Often the results were not comparable due to the different rating scales and study design. Current research on HtrA1 does not conclusively support its role as a tumor suppressor.
One-Way Functions and (Im)Perfect Obfuscation

A program obfuscator takes a program and outputs a "scrambled" version of it, where the goal is that the obfuscated program will not reveal much about its structure beyond what is apparent from executing it. There are several ways of formalizing this goal. Specifically, in indistinguishability obfuscation, first defined by Barak et al. (CRYPTO 2001), the requirement is that the results of obfuscating any two functionally equivalent programs (circuits) will be computationally indistinguishable. Recently, a fascinating candidate construction for indistinguishability obfuscation was proposed by Garg et al. (FOCS 2013). This has led to a flurry of discovery of intriguing constructions of primitives and protocols whose existence was not previously known (for instance, fully deniable encryption by Sahai and Waters, STOC 2014). Most of them explicitly rely on additional hardness assumptions, such as one-way functions. Our goal is to get rid of this extra assumption. We cannot argue that indistinguishability obfuscation of all polynomial-time circuits implies the existence of one-way functions, since if P ≠ NP, then program obfuscation (under the indistinguishability notion) is possible. Instead, the ultimate goal is to argue that if P &ne; NP and program obfuscation is possible, then one-way functions exist. Our main result is that if NP ⊈; io-BPP and there is an efficient (even imperfect) indistinguishability obfuscator, then there are one-way functions. In addition, we show that the existence of an indistinguishability obfuscator implies (unconditionally) the existence of SZK-arguments for NP. This, in turn, provides an alternative version of our main result, based on the assumption of hard-on-the average NP problems. To get some of our results we need obfuscators for simple programs such as 3CNF formulas
High Frequency of Mutator Strains among Human Uropathogenic Escherichia coli Isolates

ABSTRACT By using a panel of 603 commensal and pathogenic Escherichia coli and Shigella isolates, we showed that mutation rates of strains vary considerably among different ecotypes. Uropathogenic strains had the highest frequency of mutators, while strains from patients with bacteremia had the lowest mutation rates. No correlation between the mutation rates and antibiotic resistance was observed among the studied strains.
The global satellite mapping of precipitation (GSMaP) project

Precipitation is one of the most important parameters on the earth system, and the global distribution of precipitation and its change are essential data for modeling the water cycle, maintaining the ecosystem environment, agricultural production, improvements of the weather forecast precision, flood warning and so on. In the GPM (Global Precipitation Measurement) project, the microwave radiometers observing microwave emission from rain will be placed on many low-orbit satellites, to reduce the interval to about 3 hours in observation time for each location on the earth. Although the GPM can provide the global precipitation fields with 3 hour resolution, the precipitation map with higher resolution (< 1 hour) is required for some operational users such as flash flood warning systems and also the monthly based precipitation map is required from the climatology studies. In this presentation, the GSMaP_MVK which is a product of surface rainfall rate with 0.1 degree and 1 hour resolution on a global basis and GSMaP_Gauge which is a gauge adjusted product to the GSMaP_MVK for climatological studies are introduced, focusing particularly on structure and performance of the algorithm and some initial evaluation tests.
Ventral pallidal neurons code incentive motivation: amplification by mesolimbic sensitization and amphetamine

Neurons in ventral pallidum fire to reward and its predictive cues. We tested mesolimbic activation effects on neural reward coding. Rats learned that a Pavlovian conditioned stimulus (CS+1 tone) predicted a second conditioned stimulus (CS+2 feeder click) followed by an unconditioned stimulus (UCS sucrose reward). Some rats were sensitized to amphetamine after training. Electrophysiological activity of ventral pallidal neurons to stimuli was later recorded under the influence of vehicle or acute amphetamine injection. Both sensitization and acute amphetamine increased ventral pallidum firing at CS+2 (population code and rate code). There were no changes at CS+1 and minimal changes to UCS. With a new ‘Profile Analysis’, we show that mesolimbic activation by sensitization/amphetamine incrementally shifted neuronal firing profiles away from prediction signal coding (maximal at CS+1) and toward incentive coding (maximal at CS+2), without changing hedonic impact coding (maximal at UCS). This pattern suggests mesolimbic activation specifically amplifies a motivational transform of CS+ predictive information into incentive salience coded by ventral pallidal neurons. Our results support incentive‐sensitization predictions and suggest why cues temporally proximal to drug presentation may precipitate cue‐triggered relapse in human addicts.
A New Surgical Technique of Pancreaticoduodenectomy with Splenic Artery Resection for Ductal Adenocarcinoma of the Pancreatic Head and/or Body Invading Splenic Artery: Impact of the Balance between Surgical Radicality and QOL to Avoid Total Pancreatectomy

For pancreatic ductal adenocarcinoma (PDAC) of the head and/or body invading the splenic artery (SA), we developed a new surgical technique of proximal subtotal pancreatectomy with splenic artery and vein resection, so-called pancreaticoduodenectomy with splenic artery resection (PD-SAR). We retrospectively reviewed a total of 84 patients with curative intent pancreaticoduodenectomy (PD) for PDAC of the head and/or body. These 84 patients were classified into the two groups: conventional PD (n = 66) and PD-SAR (n = 18). Most patients were treated by preoperative chemoradiotherapy (CRT). Postoperative MDCT clearly demonstrated enhancement of the remnant pancreas at 1 and 6 months in all patients examined. Overall survival rates were very similar between PD and PD-SAR (3-year OS: 23.7% versus 23.1%, P = 0.538), despite the fact that the tumor size and the percentages of UICC-T4 determined before treatment were higher in PD-SAR. Total daily insulin dose was significantly higher in PD-SAR than in PD at 1 month, while showing no significant differences between the two groups thereafter. PD-SAR with preoperative CRT seems to be promising surgical strategy for PDAC of head and/or body with invasion of the splenic artery, in regard to the balance between operative radicality and postoperative QOL.
Plasma glucagon-like peptide 1 and peptide YY levels are not altered in symptomatic fructose-sorbitol malabsorption

Objective. Carbohydrate malabsorption causes more symptoms in patients with functional gastrointestinal disorders than in healthy individuals. The purpose of this study was to investigate whether this could be explained by differences in ileal brake hormone secretion. Material and methods. Eighteen consecutive patients with functional abdominal complaints, referred to our clinic for investigation of self-reported food hypersensitivity, were included in the study and compared with 15 healthy volunteers. All subjects ingested a mixture of 25 g fructose and 5 g sorbitol. Pulmonary hydrogen and methane excretion and plasma glucagon-like peptide 1 (GLP-1) and peptide YY (PYY) levels were measured during the next 3 h. Both habitual and post-test symptoms were assessed. Results. Malabsorption of fructose and sorbitol was present in 61% of the patients and 73% of the controls. Nevertheless, the patients experienced significantly more symptoms following carbohydrate challenge, and 78% of the patients claimed that the challenge replicated their habitual gastrointestinal complaints. No significant differences in gas excretion or GLP-1 and PYY levels were found between patients and controls or between symptomatic and asymptomatic carbohydrate malabsorbers. A weak correlation between hydrogen excretion and PYY levels was demonstrated in non-producers of methane. Conclusions. Neither intestinal gas production nor ileal brake hormone secretion seems to play a role in the symptomatology of carbohydrate intolerance in patients with self-reported food hypersensitivity. Other mechanisms related to bacterial fermentation may be involved and should be investigated further.
Differential media for quantitative recovery of waterborne Aeromonas hydrophila

Because of the ubiquity of Aeromonas spp. , their prevalence in drinking water, and the increasing number of reports on Aeromonas sp. -related infections, a standard method for routine and quantitative recovery had to be defined. On the basis of a survey of 10 media for recovery analysis and subsequent differentiation assays in mixed cultures, we conclude that ampicillin-dextrin agar performed the best for the recovery of Aeromonas spp. in drinking water and the differentiation by simple criteria of that genus from other common waterborne bacteria.
The Use of Aloe Vera Extract as a Novel Storage Media for the Avulsed Tooth

Background: Tooth avulsion is one of the most severe dental traumas which most often occur in children. When immediate replantation is not possible, storage in a proper media may lead to a prolonged survival rate. Aloe Vera is a cactus like plant with green, tapered leaves that are filled with a transparent viscous gel. This medicinal plant has significant anti-inflammatory, antioxidant, antibacterial and antifungal effects. The purpose of this study was to assess the effectiveness of different concentrations of Aloe Vera extract compared to DMEM (cell culture medium) and egg white. Methods: The periodontal ligament (PDL) cells were cultured and certain number of cells were treated with Aloe Vera extract (in four different concentrations), egg white and culture media for 1, 3, 6, and 9 hours. Cell viability was determined by using the (3-[4, 5-dimethylthiazolyl-2]-2, 5-diphenyltetrazolium bromide) assay. Moreover, One-way ANOVA and post hoc (LSD) test were used for analyzing the study groups. Results: The results indicate that culture media and Aloe Vera extract (10, 30, and 50% concentration) were statistically similar and significantly preserved more PDL cells compared to other experimental storage media. Conclusion: Aloe Vera 10, 30, and 50% may be recommended as a suitable storage media for avulsed teeth.
Possible and Certain SQL Key

Driven by the dominance of the relational model, the requirements of modern applications, and the veracity of data, we revisit the fundamental notion of a key in relational databases with NULLs. In SQL database systems primary key columns are NOT NULL by default. NULL columns may occur in unique constraints which only guarantee uniqueness for tuples which do not feature null markers in any of the columns involved, and therefore serve a different function than primary keys. We investigate the notions of possible and certain keys, which are keys that hold in some or all possible worlds that can originate from an SQL table, respectively. Possible keys coincide with the unique constraint of SQL, and thus provide a semantics for their syntactic definition in the SQL standard. Certain keys extend primary keys to include NULL columns, and thus form a sufficient and necessary condition to identify tuples uniquely, while primary keys are only sufficient for that purpose. In addition to basic characterization, axiomatization, and simple discovery approaches for possible and certain keys, we investigate the existence and construction of Armstrong tables, and describe an indexing scheme for enforcing certain keys. Our experiments show that certain keys with NULLs do occur in real-world databases, and that related computational problems can be solved efficiently. Certain keys are therefore semantically well-founded and able to maintain data quality in the form of Codd's entity integrity rule while handling the requirements of modern applications, that is, higher volumes of incomplete data from different formats.
Under Pressure! Nudging Electricity Consumption within Firms. Feedback from a Field Experiment

Many economists and psychologists have studied the impact of nudges on households’ pro-environmental behaviors. Interestingly, “private nudges” can be imagined for companies. Yet, studies focusing on nudging employees’ energy use are rare. The objective of our paper is to explore this issue with the help of a field experiment conducted at 47 French companies’ sites. Using a difference-in-differ-ence methodology, the effects of three nudges on employees’ energy conservation are tested. The first nudge, “moral appeal”, stresses the responsible use of energy. The second one, “social comparison”, informs employees on the energy consumption of other firms participating in the experiment. Finally, the third nudge, “stickers”, alerts employees about good energy conservation practices. Our results stress the complementarity of these nudges. When implemented alone, the three nudges have no significant effects on energy consumption. However, when the moral appeal and social comparison nudges are combined with the stickers nudge, they become effective.
The Malaria Parasite's Lactate Transporter PfFNT Is the Target of Antiplasmodial Compounds Identified in Whole Cell Phenotypic Screens

In this study the ‘Malaria Box’ chemical library comprising 400 compounds with antiplasmodial activity was screened for compounds that perturb the internal pH of the malaria parasite, Plasmodium falciparum. Fifteen compounds induced an acidification of the parasite cytosol. Two of these did so by inhibiting the parasite’s formate nitrite transporter (PfFNT), which mediates the H+-coupled efflux from the parasite of lactate generated by glycolysis. Both compounds were shown to inhibit lactate transport across the parasite plasma membrane, and the transport of lactate by PfFNT expressed in Xenopus laevis oocytes. PfFNT inhibition caused accumulation of lactate in parasitised erythrocytes, and swelling of both the parasite and parasitised erythrocyte. Long-term exposure of parasites to one of the inhibitors gave rise to resistant parasites with a mutant form of PfFNT that showed reduced inhibitor sensitivity. This study provides the first evidence that PfFNT is a druggable antimalarial target.
Role of antigen, CD8, and cytotoxic T lymphocyte (CTL) avidity in high dose antigen induction of apoptosis of effector CTL

Experimental data suggest that negative selection of thymocytes can occur as a result of supraoptimal antigenic stimulation. It is unknown, however, whether such mechanisms are at work in mature CD8+ T lymphocytes. Here, we show that CD8+ effector cytotoxic T lymphocytes (CTL) are susceptible to proliferative inhibition by high dose peptide antigen, leading to apoptotic death mediated by TNF-alpha release. Such inhibition is not reflected in the cytolytic potential of the CTL, since concentrations of antigen that are inhibitory for proliferation promote efficient lysis of target cells. Thus, although CTL have committed to the apoptotic pathway, the kinetics of this process are such that CTL function can occur before death of the CTL. The concentration of antigen required for inhibition is a function of the CTL avidity, in that concentrations of antigen capable of completely inhibiting high avidity CTL maximally stimulate low avidity CTL. Importantly, the inhibition can be detected in both activated and resting CTL. Blocking studies demonstrate that the CD8 molecule contributes significantly to the inhibitory signal as the addition of anti-CD8 antibody restores the proliferative response. Thus, our data support the model that mature CD8+ CTL can accommodate an activation signal of restricted intensity, which, if surpassed, results in deletion of that cell.
Spatiotemporal dynamics of snow erosion, deposition and horizontal mass flux

ABSTRACT The quantification of snow transport, both in wind tunnels and the field, apply particle counting methods limited to punctual sampling of relatively small volumes. Particle counting can only capture horizontal mass fluxes, failing to measure snow erosion or deposition. Herein, we present a novel low-cost sensor tool, based on a Microsoft Kinect, adapted to capture snow surface changes during snow drifting at unprecedented spatial and temporal resolutions. In the wind tunnel setting of these experiments we observe a balance between erosion and deposition at low wind speeds, while erosion is dominant at higher wind speeds. Significant differences in power spectral densities of surface mass flux and horizontal particle mass flux are observed. We show that for the saltation-length-scale parameter λ = 1, the integrated particle flux can be used to estimate the total surface mass flux in the wind tunnel. This provides an important basis to interpret mass flux measurements in the field.
Online control of simulated humanoids using particle belief propagation

We present a novel, general-purpose Model-Predictive Control (MPC) algorithm that we call Control Particle Belief Propagation (C-PBP). C-PBP combines multimodal, gradient-free sampling and a Markov Random Field factorization to effectively perform simultaneous path finding and smoothing in high-dimensional spaces. We demonstrate the method in online synthesis of interactive and physically valid humanoid movements, including balancing, recovery from both small and extreme disturbances, reaching, balancing on a ball, juggling a ball, and fully steerable locomotion in an environment with obstacles. Such a large repertoire of movements has not been demonstrated before at interactive frame rates, especially considering that all our movement emerges from simple cost functions. Furthermore, we abstain from using any precomputation to train a control policy offline, reference data such as motion capture clips, or state machines that break the movements down into more manageable subtasks. Operating under these conditions enables rapid and convenient iteration when designing the cost functions.
Ultrasound-Based Detection of Fasciculations in Healthy and Diseased Muscles

Involuntary muscle activations are diagnostic indicators of neurodegenerative pathologies. Currently detected by invasive intramuscular electromyography, these muscle twitches are found to be visible in ultrasound images. We present an automated computational approach for the detection of muscle twitches, and apply this to two muscles in healthy and motor neuron disease-affected populations. The technique relies on motion tracking within ultrasound sequences, extracting local movement information from muscle. A statistical analysis is applied to classify the movement, either as noise or as more coherent movement indicative of a muscle twitch. The technique is compared to operator identified twitches, which are also assessed to ensure operator agreement. We find that, when two independent operators manually identified twitches, higher interoperator agreement (Cohen's k) occurs when more twitches are present (k = 0.94), compared to a lower number (k = 0.49). Finally, we demonstrate, via analysis of receiver operating characteristics, that our computational technique detects muscle twitches across the entire dataset with a high degree of accuracy (0.83 <; accuracy <; 0.96).
New Insights into Acquisition, Boosting, and Longevity of Immunity to Malaria in Pregnant Women

Background. How antimalarial antibodies are acquired and maintained during pregnancy and boosted after reinfection with Plasmodium falciparum and Plasmodium vivax is unknown. Methods. A nested case-control study of 467 pregnant women (136 Plasmodium-infected cases and 331 uninfected control subjects) in northwestern Thailand was conducted. Antibody levels to P. falciparum and P. vivax merozoite antigens and the pregnancy-specific PfVAR2CSA antigen were determined at enrollment (median 10 weeks gestation) and throughout pregnancy until delivery. Results. Antibodies to P. falciparum and P. vivax were highly variable over time, and maintenance of high levels of antimalarial antibodies involved highly dynamic responses resulting from intermittent exposure to infection. There was evidence of boosting with each successive infection for P. falciparum responses, suggesting the presence of immunological memory. However, the half-lives of Plasmodium antibody responses were relatively short, compared with measles (457 years), and much shorter for merozoite responses (0.8–7.6 years), compared with PfVAR2CSA responses (36–157 years). The longer half-life of antibodies to PfVAR2CSA suggests that antibodies acquired in one pregnancy may be maintained to protect subsequent pregnancies. Conclusions. These findings may have important practical implications for predicting the duration of vaccine-induced responses by candidate antigens and supports the development of malaria vaccines to protect pregnant women.