Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of a Novel Enzyme Required for Starch Metabolism in Arabidopsis Leaves. The Phosphoglucan, Water Dikinase1[w]

The phosphorylation of amylopectin by the glucan, water dikinase (GWD; EC 2.7.9.4) is an essential step within starch metabolism. This is indicated by the starch excess phenotype of GWD-deficient plants, such as the sex1-3 mutant of Arabidopsis (Arabidopsis thaliana). To identify starch-related enzymes that rely on glucan-bound phosphate, we studied the binding of proteins extracted from Arabidopsis wild-type leaves to either phosphorylated or nonphosphorylated starch granules. Granules prepared from the sex1-3 mutant were prephosphorylated in vitro using recombinant potato (Solanum tuberosum) GWD. As a control, the unmodified, phosphate free granules were used. An as-yet uncharacterized protein was identified that preferentially binds to the phosphorylated starch. The C-terminal part of this protein exhibits similarity to that of GWD. The novel protein phosphorylates starch granules, but only following prephosphorylation with GWD. The enzyme transfers the β-P of ATP to the phosphoglucan, whereas the γ-P is released as orthophosphate. Therefore, the novel protein is designated as phosphoglucan, water dikinase (PWD). Unlike GWD that phosphorylates preferentially the C6 position of the glucose units, PWD phosphorylates predominantly (or exclusively) the C3 position. Western-blot analysis of protoplast and chloroplast fractions from Arabidopsis leaves reveals a plastidic location of PWD. Binding of PWD to starch granules strongly increases during net starch breakdown. Transgenic Arabidopsis plants in which the expression of PWD was reduced by either RNAi or a T-DNA insertion exhibit a starch excess phenotype. Thus, in Arabidopsis leaves starch turnover requires a close collaboration of PWD and GWD.
Diagnostic investigation of patients with chronic polyneuropathy: evaluation of a clinical guideline

OBJECTIVE (1) To evaluate a clinical guideline for the diagnostic investigation of patients presenting with signs and symptoms (present for longer than 6 weeks) suggesting a chronic polyneuropathy. (2) To investigate the contribution of electrophysiological studies to a focused search for aetiology in these patients. METHODS A chart review was carried out of a consecutive group of outpatients in 1993–7 at a university department of neurology, with signs and symptoms suggesting a polyneuropathy in whom the diagnostic investigation had been carried out according to a recently introduced guideline. Diagnostic tests were performed and final diagnoses were made. RESULTS Unnecessary investigations were carried out in 108 (51%) of 213 patients and too few tests in 23 (11%) of these patients. In 82 (48%) of the 172 patients who fulfilled the inclusion criteria neurophysiological tests did not contribute to the final diagnosis. Neurophysiological criteria for demyelination were fulfilled in only 13 (8%) of the 172 patients. CONCLUSION In patients presenting with signs and symptoms of chronic polyneuropathy the number of tests in the diagnostic investigation can be considerably reduced. In patients with signs and symptoms of polyneuropathy, providing the clinical phenotype is typical, in the presence of diabetes mellitus, renal failure, HIV infection, alcoholism, or use of potentially neurotoxic drugs further investigations are non-contributory. The significance of electrophysiological studies in the investigation of patients with polyneuropathy is rather to separate sensorimotor neuropathies from pure sensory neuropathies than to distinguish between demyelinating and axonal neuropathies.
Accuracy of the Piko-1 Pocket Spirometer

Background. Good asthma control is the main goal of long-term asthma treatment. According to the Global Initiative for Asthma (GINA) guidelines (www.ginasthma.com), medical professionals assess asthma control based on specific questions regarding asthma symptoms and by spirometry measuring forced expiratory volume in 1 second (FEV1). Patients trained in early self-detection of asthma exacerbations use a symptom-based questionnaire, such as the Asthma Control Test (ACT) [Nathan RA, Sorkness CA, Kosinski M, et al. Development of the Asthma Control Test. A survey for assessing asthma control. J Allergy Clin Immunol 2004; 113:59–64]. However, some patients may prefer harder indicators, like peak flow values, when considering how to act within their regular asthma self-management plan. Objectives. Monitoring of FEV1 at home could be an even more valuable alternative to recording peak flow values. The inexpensive handheld pocket spirometer “Piko-1®” offers the opportunity to monitor and store consecutive FEV1 values. This study assesses the accuracy of the Piko-1 device. Methods. Twenty volunteers tested 20 Piko-1 devices over five consecutive days. All results were compared to daily FEV1 values, as measured by a calibrated reference spirometer. Results. Overall, the accuracy was acceptable, although Piko-1 tended to underestimate FEV1 in the lower range. Moreover, there was no evidence of major heterogeneity between Piko-1 devices. Conclusion. The Piko-1 FEV1 measurements are sufficiently accurate to start a clinical trial to compare the detection of asthma exacerbations with this device and based on asthma symptoms alone.
Self-Reported Interview-Assisted Diet Records Underreport Energy Intake in Maintenance Hemodialysis Patients.

OBJECTIVES Studies suggest that maintenance hemodialysis (MHD) patients report dietary energy intakes (EIs) that are lower than what is actually ingested. Data supporting this conclusion have several important limitations. The present study introduces a novel approach of assessing underreporting of EI in MHD patients. DESIGN Comparisons of EI of free-living MHD patients determined from food records to their measured energy needs. SETTING Metabolic research ward. SUBJECTS Thirteen clinically stable MHD patients with unchanging weights whose EI was assessed by dietitian interview-assisted 3-day food records. INTERVENTION EI was compared with (1) patients' resting energy expenditure (REE), measured by indirect calorimetry, and estimated total energy expenditure (TEE) and (2) patients' dietary energy requirements (DER) measured while patients underwent nitrogen balance studies and consumed a constant energy diet in a research ward for a mean duration of 89.5 days. DER was calculated as the actual EI during the research study corrected for changes in body fat and lean body mass measured by Dual X-Ray Absorptiometry. MAIN OUTCOME MEASURE Underreporting of EI was determined by an EI:REE ratio <1.27 and an EI:TEE ratio or EI:DEE ratio <1.0. RESULTS Seven of the 13 MHD patients studied were male. Patient's ages were 47.7 ± standard deviation 9.7 years; body mass index averaged 25.4 ± 2.8 kg/m2, and dialysis vintage was 53.3 ± 37.1 months. The EI:REE ratio (1.03 ± 0.23) was significantly less than the cutoff value for underreporting of 1.27 (P = .001); 12 of 13 patients had EI:REE ratios <1.27. The mean EI:TEE ratio was significantly less than the cutoff value of 1.0 (0.73 ± 0.17, P < .0001), and 12 MHD patients had EI:TEE ratios <1.0. The EI:DER ratio was also <1.0 (0.83 ± 0.25, P = .012), and 10 MHD had EI:DER ratios <1.0. CONCLUSIONS Dietitian interview-assisted diet records by MHD patients substantially underestimate the patient's dietary EI.
Report of Altered Sensation in Patients with Cleft Lip

Objective To determine whether patients with cleft lip have normal perioral sensation. Design Each subject was carefully questioned about the following: sensation in the face at rest, light touch of different areas, and sensation in natural situations (e.g., exposure to cold weather) that reveal sensory abnormalities. A cotton-tip applicator stick was stroked lightly across the facial skin. The subject's descriptions of the evoked sensations were used to identify and outline areas with abnormal sensation. Setting Data were obtained from subjects participating in a longitudinal, university-based study of the functional outcomes of lip revision surgery. Patients Seventeen patients with cleft lip and 12 control subjects (aged 7 to 22 years, mean 12.9 years) participated. Results In contrast to control subjects, 9 of 16 patients (56%) reported loss in sensation, described as decreased touch, scratch, tickle, or tingle intensity. Six other patients (38%) reported additional sensation, described as increased scratch, tickle, or tingle intensity. In eight patients, the altered sensation was restricted to the skin area flanking and including the visible scar, encompassing no more than 25% of the total area bound by the inferior nose, nasolabial grooves and inferior vermilion. In seven patients (unilateral cleft), the altered area extended to the contralateral, noncleft side of the upper lip or onto the philtrum. Conclusions In contrast to the literature, sensation in the upper lip of many patients with cleft lip is not normal. Loss in sensation is exhibited most commonly and limited largely to the skin overlying tissues traumatized during reconstructive surgery.
The Reductase That Catalyzes Mycolic Motif Synthesis Is Required for Efficient Attachment of Mycolic Acids to Arabinogalactan*

Mycolic acids are essential components of the cell walls of bacteria belonging to the suborder Corynebacterineae, including the important human pathogens Mycobacterium tuberculosis and Mycobacterium leprae. Mycolic acid biosynthesis is complex and the target of several frontline antimycobacterial drugs. The condensation of two fatty acids to form a 2-alkyl-3-keto mycolate precursor and the subsequent reduction of this precursor represent two key and highly conserved steps in this pathway. Although the enzyme catalyzing the condensation step has recently been identified, little is known about the putative reductase. Using an extensive bioinformatic comparison of the genomes of M. tuberculosis and Corynebacterium glutamicum, we identified NCgl2385, the orthologue of Rv2509 in M. tuberculosis, as a potential reductase candidate. Deletion of the gene in C. glutamicum resulted in a slow growing strain that was deficient in arabinogalactan-linked mycolates and synthesized abnormal forms of the mycolate-containing glycolipids trehalose dicorynomycolate and trehalose monocorynomycolate. Analysis of the native and acetylated trehalose glycolipids by MALDI-TOF mass spectrometry indicated that these novel glycolipids contained an unreduced β-keto ester. This was confirmed by analysis of sodium borodeuteride-reduced mycolic acids by gas chromatography mass spectrometry. Reintroduction of the NCgl2385 gene into the mutant restored the transfer of mature mycolic acids to both the trehalose glycolipids and cell wall arabinogalactan. These data indicate that NCgl2385, which we have designated CmrA, is essential for the production of mature trehalose mycolates and subsequent covalent attachment of mycolic acids onto the cell wall, thus representing a focus for future structural and pathogenicity studies.
A case of being ‘double unlucky’

A 5-year-old girl presented with a history of global developmental delay and recurrent focal seizures since 2 years of age. Her parents had also noticed a progressive abdominal distension for the last 1 year. Physical examination revealed facial angiofibroma/adenoma sebaceum (Figure 1), blood pressure of 110/ 80 mmHg (between the 95th and 99th percentiles for age sex and height percentile) and a soft but distended abdomen with bilaterally palpable kidneys. Her laboratory investigations were unremarkable, and she had no proteinuria, microscopic haematuria or renal dysfunction. Imaging studies showed a bilateral nephromegaly with multiple cysts on ultrasonography (Figure 2) and periventricular tubers on computed tomography scan of the brain (Figure 3). In view of the presence of features of both autosomal dominant polycystic kidney disease (enlarged kidneys with multiple cysts) as well as tuberous sclerosis (facial angiofibroma/adenoma sebaceum and periventricular tubers) but absent family history of renal diseases and normal screening parental ultrasound, a clinical diagnosis of polycystic kidney disease 1/tuberous sclerosis complex 2 (TSC2) contiguous gene syndromes (PKDTS) was made. TSC2 (located at 16p13.3) and PKD1 (16p13.3) genes lie immediately adjacent to each other in a tail-to-tail configuration with ∼3 kb of genomic DNA in the intergenic region [1]. Mutation analysis has shown that 2–3% of TSC2 mutations are large genomic DNA deletions in which some part of both TSC2 and PKD1 are involved [2], leading to a novel contiguous gene syndrome PKDTS (Mendelian Inheritance of Mankind: 600273). In contrast with the typical TSC, the renal lesion in the PKDTS consists of PKD, which has an earlier onset and progresses more rapidly [3]. This feature of PKDTS also contrasts with isolated ADPKD, where onset is usually later and progression slower. To conclude, PKDTS is a distinct clinical entity and should be considered in patients with an early manifestation of PKD without a positive family history, but having clinical features of TSC.
Stress and fracture analyses of semi-elliptical surface cracks

The present paper concentrates on both elastic and elastic-plastic finite-element stress analyses of the surface crack in a plate subjected to tension and bending loads. Stress-intensity factor (K) equations that cover a wider range of crack-length-to-width ratios, than those previously developed by Newman and Raju, for various crack-depth-to-crack-length ratios and crack-depth-to-plate-thickness ratios have been developed and are presented. These equations are used in the subsequent fracture analyses of surface crack specimens subjected to tension and bending loads. From elastic-plastic finite-element analyses, the variations of a hyper-local constraint parameter (α h ) along the surface-crack front were studied to identify the region of maximum constraint and the critical fracture location. (The hyper-local constraint parameter is based on the average normal stresses acting over the plastic-zone region on a line in the crack plane perpendicular to the crack front.) The application of linear-elastic fracture mechanics to fracture of surface-crack specimens made of a high-strength D6AC steel are presented for both tension and bending loads. Two methods were used to characterize fracture: the K 2 -integral around the crack front and K at a critical fracture location (Φ c ). The critical fracture location was the location of the maximum of the product of K times α h . These two methods were used to evaluate the fracture toughness for both the crack-initiation loads and at the maximum failure load conditions. For tension and bending loads, the K 2 -integral method correlated 90% of the fracture data within ′25% in terms of load, whereas K at the critical fracture location correlated the data within ′20%.
Apigenin enhances skeletal muscle hypertrophy and myoblast differentiation by regulating Prmt7

Apigenin, a natural flavone abundant in various plant-derived foods including parsley and celery, has been shown to prevent inflammation and inflammatory diseases. However, the effect of apigenin on skeletal muscle hypertrophy and myogenic differentiation has not previously been elucidated. Here, we investigated the effects of apigenin on quadricep muscle weight and running distance using C57BL/6 mice on an accelerating treadmill. Apigenin stimulated mRNA expression of MHC (myosin heavy chain) 1, MHC2A, and MHC2B in the quadricep muscles of these animals. GPR56 (G protein-coupled receptor 56) and its ligand collagen III were upregulated by apigenin supplementation, together with enhanced PGC-1α, PGC-1α1, PGC-1α4, IGF1, and IGF2 expression. Prmt7 protein expression increased in conjunction with Akt and mTORC1 activation. Apigenin treatment also upregulated FNDC5 (fibronectin type III domain containing 5) mRNA expression and serum irisin levels. Furthermore, apigenin stimulated C2C12 myogenic differentiation and upregulated total MHC, MHC2A, and MHC2B expression. These events were attributable to an increase in Prmt7-p38-myoD expression and Akt and S6K1 phosphorylation. We also observed that Prmt7 regulates both PGC-1α1 and PGC-1α4 expression, resulting in a subsequent increase in GPR56 expression and mTORC1 activation. Taken together, these findings suggest that apigenin supplementation can promote skeletal muscle hypertrophy and myogenic differentiation by regulating the Prmt7-PGC-1α-GPR56 pathway, as well as the Prmt7-p38-myoD pathway, which may contribute toward the prevention of skeletal muscle weakness.
Question Quality in Community Question Answering Forums: a survey

Community Question Answering websites (CQA) offer a new opportunity for users to provide, search and share knowledge. Although the idea of receiving a direct, targeted response to a question sounds very attractive, the quality of the question itself can have an important effect on the likelihood of getting useful answers. High quality questions improve the CQA experience and therefore it is essential for CQA forums to better understand what characterizes questions that are more appealing for the forum community. In this survey, we review existing research on question quality in CQA websites. We discuss the possible measures of question quality and the question features that have been shown to influence question quality.
Low complexity Moore-Penrose inverse for large CoMP areas with sparse massive MIMO channel matrices

Joint transmission coordinated multipoint (JT CoMP) has been identified as a potential differentiator for future 5G radio systems due to its superior interference mitigation capabilities. Further, the combination with massive multiple-input-multiple-output (mMIMO) when a set of fixed grid of beams is used at eNodeB results in sparse overall channel matrices with a relatively low number of relevant channel components, which reduces the feedback overhead for reporting of channel state information (CSI). Although JT CoMP faces several challenges from synchronization to CSI outdating, in this paper the focus will be on complexity reduction of the precoding over large clustered cells utilizing massive MIMO. It will be derived how the typical sparse number of relevant channel components per user equipment can be exploited to reduce the number of floating point operations (FLOPs) by a factor of ten compared to state-of-the-art solutions for the calculation of the Moore Penrose pseudo inverse of the channel matrix.
Indirect controllability and indirect observability of quantum mechanical systems

In many experiments, a target quantum mechanical system is controlled and-or measured indirectly using an auxiliary quantum system. In the case of control, this means that the control action only affects the auxiliary system while the evolution of the target system is affected indirectly through the interaction with the auxiliary system. In the case of measurement, only the state of the auxiliary system can be measured, providing information on the initial state of the target system. Indirect controllability is the property of the target system of being driven between two arbitrary states while indirect observability refers to the possibility of extracting all the information on the state of the target system by measuring the auxiliary system. This paper has three main goals. First, we summarize recent notions and results introduced by us on the study of indirect controllability. Then, we present some new technical results on indirect controllability. In particular, we present a counterexample to the converse of a criterion for indirect controllability, which shows that the Lie algebraic condition introduced in this criterion is necessary but not sufficient for indirect controllability. This gives an open problem which is how to strengthen this condition to obtain a necessary and sufficient condition for indirect controllability. Lastly, we present a parallel treatment of indirect observability, give the relevant notions and definitions and relate the properties of indirect controllability and observability. Our final result says that strong notions of indirect controllability and observability are equivalent properties to complete controllability of the system. We discuss examples of physical systems which are controlled and-or measured indirectly. The research is motivated by experimental schemes of current interest
Quality and computation load reduction achieved by applying smart transcoding between CELP speech codecs

The increasing number of standardized speech codecs implies interoperability issues between networks deploying different and sometime incompatible standards. To assure interoperability, transcoding from one codec format to another is necessary at gateways between networks. This transcoding reduces speech quality, involves computation load and additive delay. Recently, a fair amount of work has been conducted on studying alternative transcoding methods reducing complexity and delay. In this context this paper further elaborates on some alternative solutions. It presents for each of them an evaluation of quality in relation with complexity reduction. The impact of frame lost and cascading transcoding on such smart solutions is also discussed. The obtained panel of results allows clear statements on the properties and highlights the interest of smart transcoding in terms of quality, complexity and delay reduction.
Correlation between env V1/V2 Region Diversification and Neutralizing Antibodies during Primary Infection by Simian Immunodeficiency Virus sm in Rhesus Macaques

ABSTRACT Evolution of the domain encoding the V1/V2 variable region of the simian immunodeficiency virus sm (SIVsm) envelope (env) gene was analyzed in relation to route of virus challenge, virus load, and neutralizing antibody (NAb) titers during primary infection of rhesus macaques with the pathogenic SIVsmE660 isolate. In this model system animals are initially infected with multiple viruses as evidenced by the presence of multiple V1/V2 genotypic variants that could be resolved by using a heteroduplex tracking assay (HTA). Overlapping subsets of the multiple variants were established in each animal. There was no selection for the establishment of specific variants in comparing intravenous- and intrarectal-challenged macaques at week 2 postinfection, suggesting that no genotypic selection occurred at the mucosal surface. There was an initial period of significant stability of the V1/V2 variants. Macaques challenged intravenously displayed subsequent V1/V2 diversification significantly earlier than macaques challenged intrarectally and well past the initial resolution of viremia. The time when SIVsmE660-specific NAbs reached a threshold titer of 100 was significantly correlated with the timing of V1/V2 diversification, even though antibodies to the Env protein could be detected much earlier. The time when NAbs reached a titer of 400 was significantly correlated with virus load late in infection. These results show that the route of infection affects the timing of V1/V2 diversification and that this diversification is correlated with the maturation of a specific NAb response. However, prior immunization capable of priming an anamnestic Env antibody response did not accelerate V1/V2 diversification. This result suggests that diversification of the SIV env V1/V2 region is the result of a type-specific antibody response.