Miracle-dz/UniFAR-FTUs huggingface dataset:
A Nonsymbiotic Root Hair Tip Growth Phenotype in NORK-Mutated Legumes: Implications for Nodulation Factor–Induced Signaling and Formation of a Multifaceted Root Hair Pocket for Bacteria

The Medicago truncatula Does not Make Infections (DMI2) mutant is mutated in the nodulation receptor-like kinase, NORK. Here, we report that NORK-mutated legumes of three species show an enhanced touch response to experimental handling, which results in a nonsymbiotic root hair phenotype. When care is taken not to induce this response, DMI2 root hairs respond morphologically like the wild type to nodulation factor (NF). Global NF application results in root hair deformation, and NF spot application induces root hair reorientation or branching, depending on the position of application. In the presence of Sinorhizobium meliloti, DMI2 root hairs make two-dimensional 180° curls but do not entrap bacteria in a three-dimensional pocket because curling stops when the root hair tip touches its own shank. Because DMI2 does not express the promoter of M. truncatula Early Nodulin11 (ENOD11) coupled to β-glucuronidase upon NF application, we propose a split in NF-induced signaling, with one branch to root hair curling and the other to ENOD11 expression.
The Slc11a1 (Nramp1) Gene Controls Efficacy of Mycobacterial Treatment of Allergic Asthma1

Genes controlling antibacterial resistance may be important in the hygiene hypothesis, which states that lack of bacterial infections during childhood would favor development of allergic disease. We, therefore, studied whether Nramp1 (Slc11a1) alleles, which determine susceptibility (Nramp1s) or resistance (Nramp1r) to intracellular bacteria, affect the efficacy of heat-killed Mycobacterium vaccae in the treatment of allergic asthma in a mouse model. Treatment of OVA-sensitized Nramp1s mice with M. vaccae suppressed airway hyperresponsiveness, airway eosinophilia, Ag-specific IgE, and IL-4 and IL-5 production after OVA aerosol challenge. In contrast, M. vaccae hardly affected these parameters in Nramp1r mice. In addition, The Nramp1 gene affected both T cell-mediated responses to M. vaccae in vivo and the level of macrophage activation after stimulation with M. vaccae in vitro. In conclusion, the efficacy of M. vaccae in preventing allergic and asthmatic manifestations in a mouse model is strongly affected by Nramp1 alleles. These findings could have important implications for the future use of mycobacteria and their components in the prevention or treatment of allergic asthma. A new link is described between genes, the environment, and the development of allergy, in which the Nramp1 gene fine tunes the hygiene hypothesis.
Speech/non-speech detection in Malay language spontaneous speech

The goal of this work is to discriminate speech and non-speech segments in Malay language spontaneous speech as speech/non-speech detection is important in many speech processing applications. Inaccurate sentence boundaries are a major cause of errors in automatic speech recognition and a preprocessing stage that segments the speech signal into periods of speech and non-speech is invaluable in improving the recognition accuracy. We proposed a combination of three audio features that is energy, zero crossing rate (ZCR) and fundamental frequency (F0) for the speech/non-speech detection as each feature has unique properties to differentiate speech and non-speech segments. Experiments are conducted on one-hour Malay language spontaneous speech consisting of more than 20,000 speech/non-speech segments. An accuracy evaluation reveals that the proposed method achieved 97.8% accuracy rate. Non-speech segments will further be used as candidates of sentence boundary in our next experiment.
Initial Report of a Variable Stiffness Duodenoscope for Use During Endoscopic Retrograde Cholangiopancreatography

Goals To evaluate a new variable stiffness duodenoscope. Background Variable stiffness colonoscopies have been in use for nearly a decade. We report the initial experience with a new, variable stiffness duodenoscope for use during endoscopic retrograde cholangiopancreatography (ERCP). Study Retrospective, single tertiary referral academic center. Among the first 50 patients to undergo ERCP with the variable stiffness cope, 3 patients in whom the variable stiffness duodenoscope was instrumental in procedural success are discussed in detail. Results In the first 50 patients in whom the variable stiffness duodenoscope was used, the variable stiffness function was critical to procedural success in 3 patients (6%). One patient had a gastric bypass with Roux-en-Y anatomy, 1 patient had a large J-shaped stomach that could not be traversed by a routine duodenoscope, and 1 patient had a duodenal stenosis that could not be traversed by a routine duodenoscope. In these 3 patients, the variable stiffness function allowed for procedure success. Conclusions Although most ERCPs can be accomplished with standard duodenoscopes, in cases in which extra endoscope stiffness was felt to be required, the variable stiffness function was extremely helpful.
Information based universal feature extraction

In many real world image based pattern recognition tasks, the extraction and usage of task-relevant features are the most crucial part of the diagnosis. In the standard approach, they mostly remain task-specific, although humans who perform such a task always use the same image features, trained in early childhood. It seems that universal feature sets exist, but they are not yet systematically found. In our contribution, we tried to find those universal image feature sets that are valuable for most image related tasks. In our approach, we trained a neural network by natural and non-natural images of objects and background, using a Shannon information-based algorithm and learning constraints. The goal was to extract those features that give the most valuable information for classification of visual objects hand-written digits. This will give a good start and performance increase for all other image learning tasks, implementing a transfer learning approach. As result, in our case we found that we could indeed extract features which are valid in all three kinds of tasks.
Obscura: A mobile game with camera based mechanics

The introduction of Augmented Reality (AR) technology in games for mobile devices has greatly improved user experience on these devices. Moving on from basic multi-touch interactions, built-in camera and gyroscope functions in mobile devices can also be harnessed to create a different interaction experience. This concept has not been fully explored or realized in the form of a game. In this paper, we introduced camera based mechanics to a new AR mobile game to create a gaming environment that immerses mobile devices with their physical surroundings. The mobile game “Obscura” was implemented with Unity3D, with a wide range of features: the use of camera and gyroscope to create movements, artificial superimposition of enemy creatures, and multi-touch interactions to create the enemy-capturing mechanics. Visual, audio and haptic feedback were also provided to the player to heighten gaming experience. By qualitative user evaluation on a target interest group, all participants responded positively to the gameplay of Obscura. An accomplished score of 5.3 out of 6 for overall game experience was achieved.
Experimental and clinical studies show that the probucol derivative AGI-1067 prevents vascular growth

AGI-1067 is a derivative of probucol that is a promising new development for the treatment of restenosis and possibly atherosclerosis. In monkeys fed a high-fat diet for 1 year, AGI-1067 prevented the development of atherosclerosis. In these monkeys, AGI-1067 lowered plasma levels of low-density lipoprotein (LDL)-cholesterol and, in contrast to probucol, was capable of increasing high-density lipoprotein (HDL)-cholesterol levels. Although AGI1067 did not have marked lipid-lowering effects in two transgenic mouse models (the LDL-receptor-deficient and apolipoprotein-E-deficient models) fed a high-fat chow, it decreased the atherosclerotic lesion area in the aorta. In a mouse model of acute inflammation, the mRNA for the pro-inflammatory vascular cell adhesion molecule-1 and monocyte chemoattractant protein-1 was upregulated and this was inhibited by AGI-1067. AGI-1067 inhibited the TNF-α induction of redox-sensitive inflammatory proteins, vascular cell adhesion molecule-1, monocyte chemoattractant protein-1 and Eselectin, in cell culture. In addition, AGI-1067 is an antioxidant. In the Canadian Antioxidant Restenosis Trial (CART-1) of AGI-1067 in percutaneous coronary interventions, AGI-1067 had no effect on LDL-cholesterol but lowered HDL-cholesterol. At 6 months follow up, the lumen area of the percutaneous coronary interventions segments was greater in patients treated with AGI1067 than in untreated patients. Restenosis rates were 37.5% in the placebo group and 26% in the AGI-1067 group. The lumen area of reference segments was reduced in the placebo group but increased with the higher doses of AGI1067. Unlike probucol, AGI-1067 did not alter QTc interval.
Study of association of IRS-1 and IRS-2 genes polymorphisms with clinical and metabolic features in women with polycystic ovary syndrome. Is there an impact?

Objective. Insulin receptor substrate (IRS) proteins are critical to signal transduction in insulin target tissues. The present study was undertaken to determine whether IRS-1 Gly972Arg and IRS-2 Gly1057Asp influence hormonal and metabolic characteristics in Greek patients with polycystic ovary syndrome (PCOS) and controls. Material and methods. One hundred and eighty-three women with PCOS and 88 healthy volunteers were enrolled. Venous blood samples were obtained for genetic study and hormonal profile, glucose, and insulin assays, on days 3 to 7 from cycling patients. DNA was extracted by whole blood samples for genotyping and detection of IRS-1 Gly972Arg and IRS-2 Gly1057Asp polymorphisms. Results. Fifty-six women with PCOS (30.60%), whereas 12 women in the control group (13.64%) carried the IRS-1 polymorphism (p = 0.0026). No statistically significant differences in genotypes or allele frequencies for IRS-2 polymorphism were observed between controls and PCOS women. No significant differences in any clinical or hormonal measures between subjects on the basis of genotype were observed, except the increased levels of fasting glucose that exhibit the carriers of the Asp allele of the IRS-2 polymorphism. Conclusions. Only the IRS-1 polymorphism is associated with increased susceptibility to PCOS in a Greek population. These loci should not be considered as major contributors to the hormonal and metabolic phenotype of PCOS.
How Replacements of the 12 Conserved Histidines of Subunit I Affect Assembly, Cofactor Binding, and Enzymatic Activity of theBradyrhizobium japonicum cbb 3-type Oxidase*

Alignments of the amino acid sequences of subunit I (FixN or CcoN) of the cbb 3-type oxidases show 12 conserved histidines. Six of them are diagnostic of heme-copper oxidases and are thought to bind the following cofactors: the low spin heme B and the binuclear high spin heme B-CuBcenter. The other six are FixN(CcoN)-specific and their function is unknown. To analyze the contribution of these 12 invariant histidines of FixN in cofactor binding and function of the Bradyrhizobium japonicum cbb 3-type oxidase, they were substituted by valine or alanine by site-directed mutagenesis. The H131A mutant enzyme had already been reported previously to be defective in oxidase assembly and function (Zufferey, R., Thöny-Meyer, L., and Hennecke, H. (1996) FEBS Lett. 394, 349–352). Four of the remaining histidines were not essential for activity or assembly (positions 226, 246, 333, and 457); by contrast, histidines 331, 410, and 418 were required both for activity and stability of the enzyme. The last group of mutant enzymes, H420A, H280A, H330A, and H316V, were assembled but not functional. To purify the latter mutant proteins and the wild-type enzyme, a six-histidine tag was added to the C terminus of subunit I. The His6-taggedcbb 3-oxidase complexes were purified 20-fold by a three-step purification protocol. With the exception of the H420A mutant oxidase, the mutant enzymes H280A, H316V, and H331A contained normal amounts of copper and heme B, and they displayed similar visible light spectroscopic characteristics like the wild-type His6-tagged enzyme. The His6-tagged H420A mutant oxidase differed from the His6-tagged wild-type protein by showing altered visible light spectroscopic characteristics. No stable mutant oxidase lacking copper or heme B was obtained. This strongly suggests that copper and heme B incorporations in subunit I are prerequisites for assembly of the enzyme.
Metabolic syndrome and cardiovascular risk among long‐term survivors of acute lymphoblastic leukaemia ‐ From the St. Jude Lifetime Cohort

Adult survivors of childhood acute lymphoblastic leukaemia (ALL) have a four‐fold excess risk of mortality from cardiovascular disease. This cardiovascular risk has not been fully characterized. ALL survivors [n = 784, median age 31·7 years (18·9–59·1)] in the St. Jude Lifetime Cohort Study underwent evaluation for cardiovascular risk and metabolic syndrome (MetS) according to National Cholesterol Education Program – Adult Treatment Panel III criteria. Comparisons were made to 777 age‐, sex‐, and race‐matched controls from the National Health and Nutrition Examination Survey (NHANES). MetS was identified in 259 survivors (33·6%) and associated with older age in 5‐year increments (relative risk [RR] 1·13, 95% confidence interval [CI] 1·06–1·19) and prior cranial radiotherapy (CRT) (with craniospinal radiation: RR 1·88, 95%CI 1·32–2·67; without: RR 1·67, 95%CI 1·26–2·23). Measures of obesity were highly prevalent among female survivors and CRT recipients. Compared to NHANES controls, ALL survivors had a higher risk of MetS (RR 1·43, 95%CI 1·22–1·69), hypertension (RR 2·43, 95%CI 2·06–2·86), low high‐density lipoprotein (RR 1·40, 95%CI 1·23–1·59), obesity (RR 1·47, 95%CI 1·29–1·68) and insulin resistance (1·64, 95%CI 1·44–1·86). This large study of clinically evaluated ALL survivors identified a high prevalence of MetS, obesity and cardiovascular risk, particularly in CRT recipients, underscoring the need for screening and aggressive reduction of modifiable risks.
Changes in breathing pattern and respiratory muscle performance parameters during difficult weaning.

OBJECTIVE This study examined, using noninvasive means, the changes in breathing pattern and inspiratory muscle pressure-time indices during difficult progressive withdrawal of pressure-support ventilation. DESIGN A prospective analysis of the temporal evolution of several respiratory variables in difficult-to-wean patients. SETTING A university hospital intensive care unit. PATIENTS A heterogeneous group of 17 patients receiving prolonged mechanical ventilation. INTERVENTIONS Daily measurements of breathing pattern and respiratory muscle performance parameters in difficult-to-wean patients. MEASUREMENTS AND MAIN RESULTS We examined breathing pattern variables, rapid shallow breathing (respiratory rate/tidal volume), tracheal occlusion pressure, maximal inspiratory pressure (P(I)max), and the tension-time index of the inspiratory muscles (TTmus = P(I)/P(I)max x Ti/Ttot) (where Ti/Ttot is inspiratory fraction of the cycle). All measurements were repeated at 24-hr intervals throughout the difficult weaning period. The patients were extubated on satisfying ten of 12 classical weaning criteria. Eleven patients were successfully weaned from mechanical ventilation while six patients were not. Weaning failure was associated with the following: a) longer periods of mechanical ventilation before weaning; b) high values of tracheal occlusion pressure, respiratory rate, minute ventilation, and effective impedance maintained throughout the difficult weaning period; and c) persistent high PaCO2 and intrinsic positive end-expiratory pressure values. As the weaning failure patients' inspiratory muscles confronted an increasing inspiratory load, values of the tension-time index of the inspiratory muscles entered or remained in the fatigue zone. In contrast, weaning success patients normalized their breathing pattern and decreased their tracheal occlusion pressure, effective impedance, and tension-time index values. CONCLUSIONS Breathing pattern alterations and respiratory muscle performance impairments lead to ventilator dependency after prolonged mechanical ventilation. The measurement of variables such as the noninvasive tracheal occlusion pressure, inspiratory power of breathing, and tension-time index of the inspiratory muscles facilitate the management of difficult-to-wean patients.
Lean, mean, lipolytic machines: lipid mobilization in rainbow trout during graded swimming

ABSTRACT The mobilization of mammalian lipid reserves is strongly stimulated during exercise to reach a maximum at moderate intensities, but the effects of swimming speed on fish lipolysis have never been quantified. Continuous infusion of 2-[3H]glycerol was used to measure the rate of appearance of glycerol or lipolytic rate (Ra glycerol) in rainbow trout kept at rest, or during graded exercise in a swim tunnel up to critical swimming speed (Ucrit). Results show that Ra glycerol is 1.67±0.18 µmol kg−1 min−1 in control animals, and remains at a steady level of 1.24±0.10 µmol kg−1 min−1 in exercising fish at all swimming intensities. Baseline lipolytic rate provides more than enough fatty acids from lipid reserves to accommodate all the oxidative fuel requirements for swimming at up to 2 body lengths per second (BL s−1), and more than 50% of the energy needed at Ucrit (3.4±0.1 BL s−1). Such ‘excess lipolysis’ also means that trout sustain high rates of fatty acid reesterification. Maintaining steady lipolysis at rest and throughout graded swimming is strikingly different from mammals that stimulate Ra glycerol by twofold to fivefold to support exercise. Instead, trout act like ‘lipolytic machines’ that do not modulate Ra glycerol even when their metabolic rate triples – a strategy that eliminates the need to increase lipolytic rate during exercise. This study also supports the notion that maintaining a high rate of reesterification (or triacylglycerol/fatty acid cycling) may be a mechanism widely used by ectotherms to achieve rapid membrane remodelling in variable environments. Summary: Rainbow trout behave like lipolytic machines that constantly mobilize lipid reserves in excess of energy requirements. High baseline lipolytic rates are not modulated by exercise, even when metabolic rate triples.
Evaluation of pregnane X receptor (PXR)-mediated CYP3A4 drug-drug interactions in drug development

The increased capacity to rapidly eliminate drugs can have a profound effect on the efficacious exposure of coadministered drugs, especially in today’s medical world of polypharmacy. There are numerous drug-drug interactions (DDIs) related to a loss of therapeutic efficacy and many of these are caused by pregnane X receptor (PXR)-mediated transcriptional activation of drug-metabolizing enzymes or drug transporters. Evaluation of PXR activation and subsequent induction of proteins involved in drug elimination and distribution have become routine in drug discovery and drug development. The assays used to evaluate PXR directly are high throughput and provide useful information on the ability of a drug’s potential to precipitate a DDI. In addition, they may serve as useful tools to support structure-activity or structure-liability relationships to eliminate or minimize the potential of new drug candidates to cause induction and, ultimately, a DDI.
Computerized Tomography Scan of the Brain in a Community Study of Neurological Impairment in Kenya

Neurological impairment is common in resource-poor countries, but its causes are not clear. Computerized tomography (CT) of the brain has been used to determine the cause of brain insults that may manifest as neurological impairments. The authors conducted a community survey in Kilifi of 10 218 children aged 6 to 9 years to detect neurological impairment. From this survey, 34 children were identified, of whom 16 had motor deficits, 11 complex partial seizures, 4 microcephaly or macrocephaly, and 3 severe developmental delay. These children were assessed with elicitation of history, physical examination, and CT scan of the brain. Sixteen (47%) of the scans showed abnormalities: cerebral atrophy (n = 9), schizencephaly (n = 3), periventricular leukomalacia (n = 2), porencephalic cyst (n = 1), and agenesis of the corpus callosum (n = 1). The minimum prevalence of abnormalities on the CT scan of the brain is 1.56 of 1000, and the prevalence of schizencephaly is 0.29 of 1000. Motor impairments were more likely to show abnormality than the other indications. CT abnormalities are common in children with neurological impairment in Kenya, but the appearances did not identify a major cause.
Individual differences in response to randomly assigned active individualized homeopathic and placebo treatment in fibromyalgia: implications of a double-blinded optional crossover design.

OBJECTIVE To assess individual difference characteristics of subgroups of patients with fibromyalgia (FM) patients with respect to the decision to stay in or switch from randomly-assigned verum or placebo treatment during an optional crossover phase of a double-blinded homeopathy study. DESIGN Double-blinded, randomized, placebo-controlled, optional crossover clinical trial. PARTICIPANTS Fifty-three (53) community-recruited patients with FM entered the optional crossover phase. INTERVENTION Two homeopaths jointly selected an individualized homeopathic remedy for all patients. The pharmacy dispensed either verum LM remedy or indistinguishable placebo in accord with randomized assignment for 4 months and the patient's optional crossover decision for an additional 2 months. OUTCOME MEASURES Patients completed a battery of baseline state/trait questionnaires, including mood, childhood neglect and abuse, and trait absorption. They rated global health (whole person-centered) and tender point pain on physical examination (disease-specific) at baseline, 3 months, and 6 months. RESULTS Rates of optional crossover from verum to placebo or placebo to verum were comparable (p = 0.6; 31%, and 41%, respectively). The switch subgroups had greater baseline psychologic issues (emotional neglect in placebo-switch; depression and anger in verum-switch). The verum-stay subgroup scored highest on treatment helpfulness and included all six exceptional responders who fell, prior to crossover, into the top terciles for improvement in both global health and pain. Patients staying in their randomly assigned groups, active or placebo (n = 34), scored significantly higher in trait absorption than did those who switched groups (n = 19). CONCLUSION Individual difference factors may predict better and poorer responders with FM to specific and nonspecific effects of homeopathic and placebo treatment.
Correlation of Atopobium vaginae Amount With Bacterial Vaginosis Markers

Objective The purpose of this study was to test the correlation of the amount of Atopobium vaginae with the most commonly used markers for bacterial vaginosis (BV). Materials and Methods We enrolled 103 nonpregnant and premenopausal women that were positive for BV by Amsel criteria and with a Nugent score higher than 3. All women were negative for yeast, Chlamydia trachomatis, Trichomonas vaginalis, and Neisseria gonorrhoeae. A. vaginae concentration was determined by quantitative polymerase chain reaction from samples of vaginal rinsings with 2 mL of sterile saline. Results There was no difference in the median values of A. vaginae concentration when comparing samples with presence or absence of each individual Amsel criterion. In the case of a higher pH cutoff value of 4.9, greater amounts of this microorganism (p = .02) were found. In addition, correlation tests showed that A. vaginae concentration is positively correlated with pH (p < .001) and with Nugent scores (p = .003). Conclusions The quantification of A. vaginae is useful for identification of the most severe cases of BV.