Miracle-dz/UniFAR-FTUs huggingface dataset:
Riboflavin and UV light treatment of platelets: a protective effect of platelet additive solution?

Pathogen reduction technologies (PRTs) increase the safety of the blood supply, but are also associated with cell damage. Our aim was to investigate the effect of Mirasol PRT on platelet (PLT) concentrates stored in plasma and whether the use of a PLT additive solution (PAS) is able to improve in vitro quality.
CALR mutation screening in pediatric primary myelofibrosis

Primary myelofibrosis (PMF) is quite rare in children. Mutations of JAK2V617F or MPLW515K/L were absent in pediatric patients with PMF according to previous studies. Recently, mutations in calreticulin (CALR) were described in adult patients with JAK2/MPL‐unmutated PMF. Our study aimed to analyze the clinical and genetic features of Chinese pediatric patients with PMF.
Utility of bone marrow aspiration and biopsy in initial staging of Ewing sarcoma

The current standard of care for initial staging of pediatric Ewing sarcoma (EWS) patients is to obtain a bilateral bone marrow aspiration and biopsy (BMAB). The incidence of bone marrow (BM) disease in patients deemed non‐metastatic by conventional and metabolic imaging and the concordance of BM positivity with other clinical characteristics are not well established.
Improved performance in protein secondary structure prediction by inhomogeneous score combination

MOTIVATION In many fields of pattern recognition, combination has proved efficient to increase the generalization performance of individual prediction methods. Numerous systems have been developed for protein secondary structure prediction, based on different principles. Finding better ensemble methods for this task may thus become crucial. Furthermore, efforts need to be made to help the biologist in the post-processing of the outputs. RESULTS An ensemble method has been designed to post-process the outputs of discriminant models, in order to obtain an improvement in prediction accuracy while generating class posterior probability estimates. Experimental results establish that it can increase the recognition rate of protein secondary structure prediction methods that provide inhomogeneous scores, even though their individual prediction successes are largely different. This combination thus constitutes a help for the biologist, who can use it confidently on top of any set of prediction methods. Moreover, the resulting estimates can be used in various ways, for instance to determine which areas in the sequence are predicted with a given level of reliability. AVAILABILITY The prediction is freely available over the Internet on the Network Protein Sequence Analysis (NPS@) WWW server at http://pbil.ibcp. fr/NPSA/npsa_server. ht ml. The source code of the combiner can be obtained on request for academic use.
Two Redundant Receptor-Like Cytoplasmic Kinases Function Downstream of Pattern Recognition Receptors to Regulate Activation of SA Biosynthesis1[OPEN]

Receptor-like cytoplasmic kinases PCRK1 and PCRK2 transduce defense signals from pattern recognition receptors to activate pathogen-induced SA biosynthesis. Salicylic acid (SA) serves as a critical signaling molecule in plant defense. Two transcription factors, SARD1 and CBP60g, control SA biosynthesis through regulating pathogen-induced expression of Isochorismate Synthase1, which encodes a key enzyme for SA biosynthesis. Here, we report that Pattern-Triggered Immunity Compromised Receptor-like Cytoplasmic Kinase1 (PCRK1) and PCRK2 function as key regulators of SA biosynthesis. In the pcrk1 pcrk2 double mutant, pathogen-induced expression of SARD1, CBP60g, and ICS1 is greatly reduced. The pcrk1 pcrk2 double mutant, but neither of the single mutants, exhibits reduced accumulation of SA and enhanced disease susceptibility to bacterial pathogens. Both PCRK1 and PCRK2 interact with the pattern recognition receptor FLS2, and treatment with pathogen-associated molecular patterns leads to rapid phosphorylation of PCRK2. Our data suggest that PCRK1 and PCRK2 function downstream of pattern recognition receptor in a signal relay leading to the activation of SA biosynthesis.
Bone marrow transplantation for non‐malignant diseases using treosulfan‐based conditioning

Treosulfan (treo) is an alkylating agent with a low acute toxicity profile that is increasingly used in hematopoietic stem cell transplantation, predominantly in non‐malignant diseases. Treosulfan is usually combined with additional agents, but there is scant evidence to allow comparison between different conditioning protocols using treosulfan. We present the experience of three pediatric transplantation centers in Israel using different treosulfan‐based conditioning regimens.
Contributors to Reunification or Permanent Out-of-Home Care for Physically Abused Children

This paper presents data on the outcomes of reunification or permanent out-of-home plans from physical abuse cases served under permanency planning. Client and service characteristics discriminated between placement outcomes with more severe abuse; the child's older age, poor school behavior, lower SES, and intensive contract services associated with permanent out-of-home placement and intensive direct services associated with reunification. Implications for service delivery are discussed.
Negative Regulation of Autophagy by Sulfide Is Independent of Reactive Oxygen Species1

Sulfide, but not other sulfur-containing molecules, represses autophagy irrespective of the redox conditions. Accumulating experimental evidence in mammalian, and recently plant, systems has led to a change in our understanding of the role played by hydrogen sulfide in life processes. In plants, hydrogen sulfide mitigates stress and regulates important plant processes such as photosynthesis, stomatal movement, and autophagy, although the underlying mechanism is not well known. In this study, we provide new experimental evidence that, together with our previous findings, demonstrates the role of hydrogen sulfide in regulating autophagy. We used green fluorescent protein fluorescence associated with autophagic bodies and immunoblot analysis of the ATG8 protein to show that sulfide (and no other molecules such as sulfur-containing molecules or ammonium) was able to inhibit the autophagy induced in Arabidopsis (Arabidopsis thaliana) roots under nitrogen deprivation. Our results showed that sulfide was unable to scavenge reactive oxygen species generated by nitrogen limitation, in contrast to well-established reducers. In addition, reducers were unable to inhibit the accumulation of autophagic bodies and ATG8 protein forms to the same extent as sulfide. Therefore, we conclude that sulfide represses autophagy via a mechanism that is independent of redox conditions.
Alarm Photosynthesis: Calcium Oxalate Crystals as an Internal CO2 Source in Plants1

A new photosynthetic path named “alarm photosynthesis” uses mesophyll calcium oxalate crystals as the CO2 source when stomata are closed, providing adaptive advantages under drought conditions. Calcium oxalate crystals are widespread among animals and plants. In land plants, crystals often reach high amounts, up to 80% of dry biomass. They are formed within specific cells, and their accumulation constitutes a normal activity rather than a pathological symptom, as occurs in animals. Despite their ubiquity, our knowledge on the formation and the possible role(s) of these crystals remains limited. We show that the mesophyll crystals of pigweed (Amaranthus hybridus) exhibit diurnal volume changes with a gradual decrease during daytime and a total recovery during the night. Moreover, stable carbon isotope composition indicated that crystals are of nonatmospheric origin. Stomatal closure (under drought conditions or exogenous application of abscisic acid) was accompanied by crystal decomposition and by increased activity of oxalate oxidase that converts oxalate into CO2. Similar results were also observed under drought stress in Dianthus chinensis, Pelargonium peltatum, and Portulacaria afra. Moreover, in A. hybridus, despite closed stomata, the leaf metabolic profiles combined with chlorophyll fluorescence measurements indicated active photosynthetic metabolism. In combination, calcium oxalate crystals in leaves can act as a biochemical reservoir that collects nonatmospheric carbon, mainly during the night. During the day, crystal degradation provides subsidiary carbon for photosynthetic assimilation, especially under drought conditions. This new photosynthetic path, with the suggested name “alarm photosynthesis,” seems to provide a number of adaptive advantages, such as water economy, limitation of carbon losses to the atmosphere, and a lower risk of photoinhibition, roles that justify its vast presence in plants.
Primary and revision efficacy of cross-wired metallic stents for endoscopic bilateral stent-in-stent placement in malignant hilar biliary strictures

Background and study aims: Endoscopic bilateral drainage for inoperable malignant hilar biliary strictures (HBS) using metal stents is considered to be technically difficult. Furthermore, endoscopic revision of bilateral stenting after occlusion can be challenging. This study was performed to evaluate the long-term efficacy of endoscopic bilateral stent-in-stent placement of cross-wired metallic stents in high-grade malignant HBS and planned endoscopic bilateral revision. Patients and methods: A total of 84 patients with inoperable high-grade malignant HBS were enrolled from three academic tertiary referral centers. Two cross-wired metal stents were inserted using a bilateral stent-in-stent placement method. Bilateral endoscopic revision was also performed during follow-up using either identical metal stents or plastic stents. The main outcome measurements were technical and functional success, complications, stent patency, and endoscopic revision efficacy. Results: The technical and clinical success rates of endoscopic bilateral stent-in-stent placement of cross-wired metallic stents were 95.2 % (80 /84) and 92.9 % (78 /84), respectively. Median patency (range) and survival were 238 days (10 – 429) and 256 days (10 – 1130), respectively. Obstruction of primary bilateral stents occurred in 30.8 % (24 /78) of patients with functionally successful stent placement. The technical and clinical success rates of planned bilateral endoscopic revision for occluded stents were 83.3 % (20 /24) and 79.2 % (19 /24), respectively. For revision, bilateral metallic stents were placed in 11 patients (55.0 %); the remaining patients received plastic stents. Conclusions: Palliative endoscopic bilateral stent-in-stent placement of cross-wired metallic stents was effective in patients with inoperable HBS. Revision endoscopic bilateral stenting may be feasible and successful in cases where the primary deployed metal stents are occluded.
Modularity of Conifer Diterpene Resin Acid Biosynthesis: P450 Enzymes of Different CYP720B Clades Use Alternative Substrates and Converge on the Same Products1[OPEN]

Diterpene resin acids are major conifer defense compounds and important precursors for industrial bioproducts and are formed through a modular system of diterpene synthases and cytochrome P450s. Cytochrome P450 enzymes of the CYP720B subfamily play a central role in the biosynthesis of diterpene resin acids (DRAs), which are a major component of the conifer oleoresin defense system. CYP720Bs exist in families of up to a dozen different members in conifer genomes and fall into four different clades (I–IV). Only two CYP720B members, loblolly pine (Pinus taeda) PtCYP720B1 and Sitka spruce (Picea sitchensis) PsCYP720B4, have been characterized previously. Both are multisubstrate and multifunctional clade III enzymes, which catalyze consecutive three-step oxidations in the conversion of diterpene olefins to DRAs. These reactions resemble the sequential diterpene oxidations affording ent-kaurenoic acid from ent-kaurene in gibberellin biosynthesis. Here, we functionally characterized the CYP720B clade I enzymes CYP720B2 and CYP720B12 in three different conifer species, Sitka spruce, lodgepole pine (Pinus contorta), and jack pine (Pinus banksiana), and compared their activities with those of the clade III enzymes CYP720B1 and CYP720B4 of the same species. Unlike the clade III enzymes, clade I enzymes were ultimately found not to be active with diterpene olefins but converted the recently discovered, unstable diterpene synthase product 13-hydroxy-8(14)-abietene. Through alternative routes, CYP720B enzymes of both clades produce some of the same profiles of conifer oleoresin DRAs (abietic acid, neoabietic acid, levopimaric acid, and palustric acid), while clade III enzymes also function in the formation of pimaric acid, isopimaric acid, and sandaracopimaric acid. These results highlight the modularity of the specialized (i.e. secondary) diterpene metabolism, which produces conifer defense metabolites through variable combinations of different diterpene synthase and CYP720B enzymes.
Effect of Fermentation by Probiotic Lactobacillus acidophilus NCDC 13 on Nutritional Profile of a Dairycereal based Composite Substrate

Effect of Fermentation by Probiotic Lactobacillus acidophilus NCDC 13 on Nutritional Profile of a Dairycereal based Composite Substrate The current study was aimed at evaluating the effects of fermentation on the nutritional profile of a composite dairy-cereal substrate. The organism (Lactobacillus acidophilus NCDC 13, a dairy isolate probiotic strain) had a biomass concentration 1012/ml in MRS medium and was starch hydrolysis-negative and phytasepositive with a phytase activity of 0.705 unit/ h/ ml.
Journal of Informetrics

an explosive rate in cyberspace, and negative comments could be very harmful to an enterprise. Lately, researchers have been paying much attention to sentiment classiﬁcation. The goalistoefﬁcientlyidentifytheemotionsoftheircustomerstoallowcompaniestorespond intheappropriatemannertowhatcustomershavetosay.Semanticorientationindexesand machine learning methods are usually employed to achieve this goal. Semantic orientation indexes do not have good performance, but they return results quickly. Machine learning techniques provide better classiﬁcation accuracy, but require a lot of training time. In order to combine the advantages of these two methods, this study proposed a neural-network based approach. It uses semantic orientation indexes as inputs for the neural networks to determine the sentiments of the bloggers quickly and effectively. Several actual blogs are used to evaluate the effectiveness of our approach. The experimental results indicate that the proposed approach outperforms traditional approaches including other neural networks and several semantic orientation indexes. © 2011 Elsevier Ltd. All rights reserved.
The impact of fetal and maternal physiologic factors on umbilical cord blood quality as a source of stem cells in Egyptian population

Umbilical cord blood (UCB) has rapidly become a clinically useful alternative stem cell source. Many variables have been used to evaluate a UCB unit and predict transplant outcomes. The objective of this study was to measure the expression of hematopoietic stem cells in UCB and its relation to certain maternal and neonatal physiologic factors to establish optimum criteria for UCB donor selection.
Cellulose Deficiency Is Enhanced on Hyper Accumulation of Sucrose by a H+-Coupled Sucrose Symporter1[OPEN]

The cellulose deficiency of the shv3svl1 mutant is enhanced by the uptake of exogenous sucrose, which results in carbon redirection from cellulose to starch biosynthesis. In order to understand factors controlling the synthesis and deposition of cellulose, we have studied the Arabidopsis (Arabidopsis thaliana) double mutant shaven3 shaven3-like1 (shv3svl1), which was shown previously to exhibit a marked cellulose deficiency. We discovered that exogenous sucrose (Suc) in growth medium greatly enhances the reduction in hypocotyl elongation and cellulose content of shv3svl1. This effect was specific to Suc and was not observed with other sugars or osmoticum. Live-cell imaging of fluorescently labeled cellulose synthase complexes revealed a slowing of cellulose synthase complexes in shv3svl1 compared with the wild type that is enhanced in a Suc-conditional manner. Solid-state nuclear magnetic resonance confirmed a cellulose deficiency of shv3svl1 but indicated that cellulose crystallinity was unaffected in the mutant. A genetic suppressor screen identified mutants of the plasma membrane Suc/H+ symporter SUC1, indicating that the accumulation of Suc underlies the Suc-dependent enhancement of shv3svl1 phenotypes. While other cellulose-deficient mutants were not specifically sensitive to exogenous Suc, the feronia (fer) receptor kinase mutant partially phenocopied shv3svl1 and exhibited a similar Suc-conditional cellulose defect. We demonstrate that shv3svl1, like fer, exhibits a hyperpolarized plasma membrane H+ gradient that likely underlies the enhanced accumulation of Suc via Suc/H+ symporters. Enhanced intracellular Suc abundance appears to favor the partitioning of carbon to starch rather than cellulose in both mutants. We conclude that SHV3-like proteins may be involved in signaling during cell expansion that coordinates proton pumping and cellulose synthesis.
Uncoupling High Light Responses from Singlet Oxygen Retrograde Signaling and Spatial-Temporal Systemic Acquired Acclimation1[OPEN]

Uncoupling high light signal perception from distal signal reception shows that 1O2 EXECUTER-dependent retrograde signaling is required for initiation of systemic acquired acclimation in Arabidopsis. Distinct ROS signaling pathways initiated by singlet oxygen (1O2) or superoxide and hydrogen peroxide have been attributed to either cell death or acclimation, respectively. Recent studies have revealed that more complex antagonistic and synergistic relationships exist within and between these pathways. As specific chloroplastic ROS signals are difficult to study, rapid systemic signaling experiments using localized high light (HL) stress or ROS treatments were used in this study to uncouple signals required for direct HL and ROS perception and distal systemic acquired acclimation (SAA). A qPCR approach was chosen to determine local perception and distal signal reception. Analysis of a thylakoidal ascorbate peroxidase mutant (tapx), the 1O2-retrograde signaling double mutant (ex1/ex2), and an apoplastic signaling double mutant (rbohD/F) revealed that tAPX and EXECUTER 1 are required for both HL and systemic acclimation stress perception. Apoplastic membrane-localized RBOHs were required for systemic spread of the signal but not for local signal induction in directly stressed tissues. Endogenous ROS treatments revealed a very strong systemic response induced by a localized 1 h induction of 1O2 using the conditional flu mutant. A qPCR time course of 1O2 induced systemic marker genes in directly and indirectly connected leaves revealed a direct vascular connection component of both immediate and longer term SAA signaling responses. These results reveal the importance of an EXECUTER-dependent 1O2 retrograde signal for both local and long distance RBOH-dependent acclimation signaling that is distinct from other HL signaling pathways, and that direct vascular connections have a role in spatial-temporal SAA induction.
The ROS Wheel: Refining ROS Transcriptional Footprints1[OPEN]

Transcriptional footprints during oxidative stress in Arabidopsis. In the last decade, microarray studies have delivered extensive inventories of transcriptome-wide changes in messenger RNA levels provoked by various types of oxidative stress in Arabidopsis (Arabidopsis thaliana). Previous cross-study comparisons indicated how different types of reactive oxygen species (ROS) and their subcellular accumulation sites are able to reshape the transcriptome in specific manners. However, these analyses often employed simplistic statistical frameworks that are not compatible with large-scale analyses. Here, we reanalyzed a total of 79 Affymetrix ATH1 microarray studies of redox homeostasis perturbation experiments. To create hierarchy in such a high number of transcriptomic data sets, all transcriptional profiles were clustered on the overlap extent of their differentially expressed transcripts. Subsequently, meta-analysis determined a single magnitude of differential expression across studies and identified common transcriptional footprints per cluster. The resulting transcriptional footprints revealed the regulation of various metabolic pathways and gene families. The RESPIRATORY BURST OXIDASE HOMOLOG F-mediated respiratory burst had a major impact and was a converging point among several studies. Conversely, the timing of the oxidative stress response was a determining factor in shaping different transcriptome footprints. Our study emphasizes the need to interpret transcriptomic data sets in a systematic context, where initial, specific stress triggers can converge to common, aspecific transcriptional changes. We believe that these refined transcriptional footprints provide a valuable resource for assessing the involvement of ROS in biological processes in plants.
Participation in pediatric oncology research protocols: Racial/ethnic, language and age‐based disparities

Survival rates in pediatric oncology have improved dramatically, in part due to high patient participation in clinical trials. Although racial/ethnic inequalities in clinical trial participation have been reported in adults, pediatric data and studies comparing participation rates by socio‐demographic characteristics are scarce. The goal of this study was to assess differences in research protocol participation for childhood cancer by age, sex, race/ethnicity, parental language, cancer type, and insurance status.
Metabolomics in transfusion medicine

Biochemical investigations on the regulatory mechanisms of red blood cell (RBC) and platelet (PLT) metabolism have fostered a century of advances in the field of transfusion medicine. Owing to these advances, storage of RBCs and PLT concentrates has become a lifesaving practice in clinical and military settings. There, however, remains room for improvement, especially with regard to the introduction of novel storage and/or rejuvenation solutions, alternative cell processing strategies (e.g., pathogen inactivation technologies), and quality testing (e.g., evaluation of novel containers with alternative plasticizers). Recent advancements in mass spectrometry–based metabolomics and systems biology, the bioinformatics integration of omics data, promise to speed up the design and testing of innovative storage strategies developed to improve the quality, safety, and effectiveness of blood products.