Miracle-dz/UniFAR-FTUs huggingface dataset:
Reference-Driven Undersampled MR Image Reconstruction Using Wavelet Sparsity-Constrained Deep Image Prior

Deep learning has shown potential in significantly improving performance for undersampled magnetic resonance (MR) image reconstruction. However, one challenge for the application of deep learning to clinical scenarios is the requirement of large, high-quality patient-based datasets for network training. In this paper, we propose a novel deep learning-based method for undersampled MR image reconstruction that does not require pre-training procedure and pre-training datasets. The proposed reference-driven method using wavelet sparsity-constrained deep image prior (RWS-DIP) is based on the DIP framework and thereby reduces the dependence on datasets. Moreover, RWS-DIP explores and introduces structure and sparsity priors into network learning to improve the efficiency of learning. By employing a high-resolution reference image as the network input, RWS-DIP incorporates structural information into network. RWS-DIP also uses the wavelet sparsity to further enrich the implicit regularization of traditional DIP by formulating the training of network parameters as a constrained optimization problem, which is solved using the alternating direction method of multipliers (ADMM) algorithm. Experiments on in vivo MR scans have demonstrated that the RWS-DIP method can reconstruct MR images more accurately and preserve features and textures from undersampled k-space measurements.
Single-Molecule Spectroscopic Tools for Measuring Microsecond to Millisecond Dynamics of Calmodulin

E. Shane Price, Ph.D. Department of Chemistry, August 25, 2009 University of Kansas Single-molecule spectroscopy has developed into a powerful tool for the study of biological systems. The ability to observe single protein changes has revealed a great deal of information about the heterogeneity of these systems. In this dissertation, single-molecule techniques have been used to investigate the effect of Ca on millisecond and microsecond fluctuations of the protein calmodulin (CaM). The first part of this dissertation discusses the development and testing of a home-built, two-channel, confocal microscope system used for fluorescence correlation spectroscopy (FCS) and scanning single-molecule measurements. Secondly, the newly built system was tested by performing two-channel FCS measurements using a FRET-pair labeled synthetic polyproline peptide. Polyproline has been shown to approximate a “rigid-rod” and therefore was not expected to show any FRET fluctuations on the FCS timescale. The results from the polyproline correlations led to an investigation to develop expressions to describe the differences in the initial amplitudes of the correlations. These expressions were dependent on the presence of multiple FRET states in the solution and fits were demonstrated using both simulations and real data. Next, the dynamics of several FRET-pair labeled mutants of CaM were measured using FCS techniques. The resulting correlations were globally fit to reveal inter-lobe dynamics on the 100 microsecond timescale that were diminished upon the
The Safety of Baduanjin Exercise: A Systematic Review

Objectives Baduanjin exercise is a form of Qigong exercise therapy that has become increasingly popular worldwide. The aims of the current systematic review were to summarize reported adverse events potentially associated with Baduanjin exercise based on currently available literature and to evaluate the quality of the methods used to monitor adverse events in the trials assessed. Methods The English databases PubMed, Cochrane library, and EMbase were searched from inception to October 2020 using the keywords “Baduanjin” or “eight session brocade. ” Only studies that included Baduanjin exercise therapy were included. Results Forty-seven trials with a total of 3877 participants were included in this systematic review. Twenty-two studies reported protocols for monitoring adverse events, and two studies reported the occurrence of adverse events during training. The adverse events reported included palpitation, giddiness, knee pain, backache, fatigue, nervousness, dizziness, shoulder pain, chest tightness, shortness of breath, and muscle ache. Conclusions Only two studies reported adverse events that were potentially caused by Baduanjin exercise. Adverse events related to Baduanjin exercise in patients with chronic fatigue syndrome may include muscle ache, palpitation, giddiness, knee pain, backache, fatigue, nervousness, dizziness, shoulder pain, chest tightness, and shortness of breath. Further studies conducted in accordance with the Consolidated Standards of Reporting Trials statement guideline incorporating monitoring of adverse events are recommended. Additional clinical trials in which Baduanjin exercise is used as a main intervention are needed, and further meta-analysis may be required to assess its safety and reach more informed conclusions in this regard in the future.
The Level of Unmet Need for Family Planning and Its Predictors among HIV-Positive Women in Ethiopia: A Systematic Review and Meta-Analysis

Background Studies indicated that the need for family planning appears to be greater for human immuno-deficiency virus- (HIV-) positive women than the general population to reduce the risk of pediatrics HIV infection and related consequences of unintended pregnancy. We aimed to assess the level of unmet need for family planning and its predictors among HIV-positive women in Ethiopia. Methods Online databases such as PubMed, SCOPUS, EMBASE, HINARI, Google Scholar, and digital libraries of universities were used to search for studies to be included in this systematic review and meta-analysis. Quality assessment of included studies was conducted using the Newcastle-Ottawa Quality Assessment Scale (NOS). Data were extracted using the format prepared on Excel workbook and analyzed by the Stata 11 software. Cochran (Q test) and I2 test statistics were used to assess the heterogeneity of studies. Similarly, the funnel plot and Egger's regression asymmetry test were used to assess publication bias. Result This systematic review and meta-analysis was conducted using nine primary studies with a total of 6,154 participants. The pooled prevalence of unmet need for family planning among HIV-positive women was found to be 25.72% (95% CI: 21.63%, 29.81%). Participants age 15-24 years ((OR = 3.12; 95% CI: 1.59, 6.11) I2 = 27.5%; p = 0.252), being illiterate ((OR = 2.69; 95% CI: 1.69, 4.26) I2 = 0.0%; p = 0.899), failure to discuss FP with partner ((OR = 3.38; 95% CI: 2.20, 5.18) I2 = 0.0%; p = 0.861), and no access to family planning information ((OR = 4.70; 95% CI: 2.83, 7.81) I2 = 0.0%; p = 0.993) were found to be a significant predictors of unmet need for family planning among HIV-positive women. Conclusion The level of unmet need for family planning among HIV-positive women was found to be high in Ethiopia. Being young age, illiteracy, failed to discuss family planning issues with a partner, and no access to family planning information were found to be the significant predictors of unmet need for family planning among HIV-positive women in Ethiopia. Improving information access and encouraging partners' involvement in family planning counseling and services could reduce the level of unmet need for family planning.
The RITE of Passage: Learning Styles and Residency In-Service Training Examination (RITE) Scores

Introduction The objective of the pilot study was to determine the association between learning preferences and improvement in the American Academy of Neurology Residency In-Service Training Examination (RITE) scores from postgraduate year 2 (PGY-2) to postgraduate year 3 (PGY-3) in neurology residents. Methods Neurology residents at the University of Florida were approached to participate, and their consent was obtained. VARK inventory, representing four modalities (visual, aural, read/write, kinesthetic) of learning preferences, was completed by participants. Participants could pick more than one modality. The number of responses in each sensory domain was recorded, with higher numbers indicating stronger preference. Residents’ performance on the RITE was recorded for PGY-2 and PGY-3. Results Seventeen residents completed the VARK inventory and 16 had data for RITE. Residents demonstrated overall positive change in RITE from PGY-2 to PGY-3 (mean change = 6%; 95%CI: 4%, 9%). The median number of responses was highest for the kinesthetic domain (median = 7, range = 1-12), followed by visual (median = 6, range = 2-12), aural (median = 4, range = 1-10), and read/write (median = 4, range = 1-10). Among VARK domains, the number of responses in read/write had the strongest correlation with mean change in RITE performance from PGY-2 to PGY-3 (r = 0.45; 95%CI: -0.08, 0.78); residents in the high read/write group (number of response above median) had greater mean change in RITE performance (9%; 95%CI: 6%, 12%) while those in the low read/write group showed little to no increase in RITE from PGY-2 to PGY-3 (2%; 95%CI: -1%, 6%). Conclusions Higher VARK survey responses in the read/write domain were related to greater change in RITE scores from PGY-2 to PGY-3. These findings seem intuitively obvious considering the format of the RITE. These pilot data permit further investigation of individual resident learning preference and how it relates to test performance. By understanding a resident’s learning style, both educators and the resident will have an awareness of areas that need to be improved to be successful, which may be via remedial curricula and self-study activities.
Quyu Shengji Formula Facilitates Diabetic Wound Healing via Inhibiting the Expression of Prostaglandin Transporter

Background Quyu Shengji Formula (QSF), a Chinese medicine formula widely used in the clinic, has proven therapeutic effects on diabetic ulcers. Nevertheless, the potential mechanism of how QSF cures diabetic ulcer remains elusive. Objective To assess the mechanism of QSF against wound healing defects in diabetes. Methods Db/db mice were adopted to determine the therapeutic potential of QSF. Further histology analysis was performed by hematoxylin and eosin (H&E) staining. Moreover, the expression patterns of prostaglandin transporter (PGT), prostaglandin E2 (PGE2), and angiogenesis factor vascular endothelial growth factor (VEGF) were evaluated by immunostaining (IHC) analysis, ELISA assay, real-time quantitative polymerase chain reaction (RT-qPCR), and western blot analysis in vivo. Human dermal microvascular endothelial cells (HDMECs) and the shRNA interference technique were used to explore the effects of QSF on cell migration, PGT, PGE2, and angiogenesis factor VEGF in vitro. Results Applied QSF on the wound of db/db mice significantly accelerated wound closure. Reductions of PGT and elevations of PGE2 and increased angiogenesis factor VEGF levels were shown after QSF treatment in vivo and in vitro. Furthermore, QSF promoted HDMEC migration. Inhibition of the expression of PGT by shRNA reversed phenotypes of QSF treatment in vitro. Conclusion Taken together, our findings reveal that QSF ameliorates diabetes-associated wound healing defects by abolishing the expression of PGT.
Naturalistic Research on Recovery Processes: Looking to the Future

Because recovery is an ongoing process, conducting research on the recovery process presents multiple challenges. The process can play out over many years, but change also can occur quickly. Although researchers are keenly interested in the precursors of these sudden changes, a researcher is unlikely to be present at critical moments; however, technology offers new options not available in prior years. Recovery research at this point, however, must be pursued largely through observational methods. Experiments involving aspects of recovery can and should be done, but observation is an essential part of recovery research. Hence, this paper focuses on technologies for conducting and analyzing observational studies. The author briefly reviews methods for gathering intensive longitudinal data and discusses how recovery researchers can take advantage of existing technology to delve more deeply into the complex processes associated with recovery and relapse. The future of recovery research, however, will require examining new ways of investigating recovery phenomena, including a new option for gathering data based on decision theory. Taking maximum advantage of existing and new technology for recovery research will require increasing collaboration between recovery researchers and quantitative scientists.
Genome-wide identification, evolution, and expression of the SNARE gene family in wheat resistance to powdery mildew

SNARE proteins mediate eukaryotic cell membrane/transport vesicle fusion and act in plant resistance to fungi. Herein, 173 SNARE proteins were identified in wheat and divided into 5 subfamilies and 21 classes. The number of the SYP1 class type was largest in TaSNAREs. Phylogenetic tree analysis revealed that most of the SNAREs were distributed in 21 classes. Analysis of the genetic structure revealed large differences among the 21 classes, and the structures in the same group were similar, except across individual genes. Excluding the first homoeologous group, the number in the other homoeologous groups was similar. The 2,000 bp promoter region of the TaSNARE genes were analyzed, and many W-box, MYB and disease-related cis-acting elements were identified. The qRT-PCR-based analysis of the SNARE genes revealed similar expression patterns of the same subfamily in one wheat variety. The expression patterns of the same gene in resistant/sensitive varieties largely differed at 6 h after infection, suggesting that SNARE proteins play an important role in early pathogen infection. Here, the identification and expression analysis of SNARE proteins provide a theoretical basis for studies of SNARE protein function and wheat resistance to powdery mildew.
Leber’s Hereditary Optic Neuropathy: the roles of mitochondrial transfer RNA variants

Leber’s Hereditary Optic Neuropathy (LHON) was a common maternally inherited disease causing severe and permanent visual loss which mostly affects males. Three primary mitochondrial DNA (mtDNA) mutations, ND1 3460G>A, ND4 11778G>A and ND6 14484T>C, which affect genes encoding respiratory chain complex I subunit, are responsible for >90% of LHON cases worldwide. Families with maternally transmitted LHON show incomplete penetrance with a male preponderance for visual loss, suggesting the involvement of secondary mtDNA variants and other modifying factors. In particular, variants in mitochondrial tRNA (mt-tRNA) are important risk factors for LHON. These variants decreased the tRNA stability, prevent tRNA aminoacylation, influence the post-transcriptionalmodification and affect tRNA maturation. Failure of mt-tRNA metabolism subsequently impairs protein synthesis and expression, folding, and function of oxidative phosphorylation (OXPHOS) enzymes, which aggravates mitochondrial dysfunction that is involved in the progression and pathogenesis of LHON. This review summarizes the recent advances in our understanding of mt-tRNA biology and function, as well as the reported LHON-related mt-tRNA second variants; it also discusses the molecular mechanism behind the involvement of these variants in LHON.
A target enrichment probe set for resolving the flagellate land plant tree of life

PREMISE New sequencing technologies facilitate the generation of large‐scale molecular data sets for constructing the plant tree of life. We describe a new probe set for target enrichment sequencing to generate nuclear sequence data to build phylogenetic trees with any flagellate land plants, including hornworts, liverworts, mosses, lycophytes, ferns, and all gymnosperms. METHODS We leveraged existing transcriptome and genome sequence data to design the GoFlag 451 probes, a set of 56,989 probes for target enrichment sequencing of 451 exons that are found in 248 single‐copy or low‐copy nuclear genes across flagellate plant lineages. RESULTS Our results indicate that target enrichment using the GoFlag451 probe set can provide large nuclear data sets that can be used to resolve relationships among both distantly and closely related taxa across the flagellate land plants. We also describe the GoFlag 408 probes, an optimized probe set covering 408 of the 451 exons from the GoFlag 451 probe set that is commercialized by RAPiD Genomics. CONCLUSIONS A target enrichment approach using the new probe set provides a relatively low‐cost solution to obtain large‐scale nuclear sequence data for inferring phylogenetic relationships across flagellate land plants.
MINI REVIEW Conserved domains of glycosyltransferases

Glycosyltransferases catalyze the synthesis of glycoconjugates by transferring a properly activated sugar residue to an appropriate acceptor molecule or aglycone for chain initiation and elongation. The acceptor can be a lipid, a protein, a heterocyclic compound, or another carbohydrate residue. A catalytic reaction is believed to involve the recognition of both the donor and acceptor by suitable domains, as well as the catalytic site of the enzyme. To elucidate the structural requirements for substrate recognition and catalytic reactions of glycosyltransferases, we have searched the databases for homologous sequences, identified conserved amino acid residues, and proposed potential domain motifs for these enzymes. Depending on the configuration of the anomeric functional group of the glycosyl donor molecule and of the resulting glycoconjugate, all known glycosyltransferases can be divided into two major types: retaining glycosyltransferases, which transfer sugar residue with the retention of anomeric configuration, and inverting glycosyltransferases, which transfer sugar residue with the inversion of anomeric configuration. One conserved domain of the inverting glycosyltransferases identified in the database is responsible for the recognition of a pyrimidine nucleotide, which is either the UDP or the TDP portion of a donor sugar-nucleotide molecule. This domain is termed “Nucleotide Recognition Domain 1β,” or NRD1β, since the type of nucleotide is the only common structure among the sugar donors and acceptors. NRD1β is present in 140 glycosyltransferases. The central portion of the NRD1β domain is very similar to the domain that is present in one family of retaining glycosyltransferases. This family is termed NRD1α to designate the similarity and stereochemistry of sugar transfer, and it consists of 77 glycosyltransferases identified thus far. In the central portion there is a homologous region for these two families and this region probably has a catalytic function. A third conserved domain is found exclusively in membrane-bound glycosyltransferases and is termed NRD2; this domain is present in 98 glycosyltransferases. All three identified NRDs are present in archaebacterial, eubacterial, viral, and eukaryotic glycosyltransferases. The present article presents the alignment of conserved NRD domains and also presents a brief overview of the analyzed glycosyltransferases which comprise about 65% of all known sugar-nucleotide dependent (Leloir-type) and putative glycosyltransferases in different databases. A potential mechanism for the catalytic reaction is also proposed. This proposed mechanism should facilitate the design of experiments to elucidate the regulatory mechanisms of glycosylation reactions. Amino acid sequence information within the conserved domain may be utilized to design degenerate primers for identifying DNA encoding new glycosyltransferases.
Ambulatory blood pressure monitoring in children undergoing polysomnography

Ambulatory blood pressure monitoring (ABPM) is recommended for the diagnosis of hypertension in children at high risk, such as children with obesity or obstructive sleep apnea (OSA). Nocturnal hypertension is highly predictive of cardiovascular outcomes. ABPM allows for early detection of nocturnal hypertension in children. Although OSA is the most common sleep disorder associated with hypertension, studies have also shown an increase in cardiovascular risk in adult patients with other sleep disorders; therefore, there is an imperative need to provide early diagnosis in children at high risk. In the present study, we evaluated the feasibility of using ABPM during polysomnography (PSG) in children referred for sleep disordered breathing to the Seattle Children’s Hospital Sleep Disorders Center. A total of 41 children aged 7–18 years were included in this study. The ABPM monitor was worn for a mean (SD) of 10.2 (1.5) hr. No significant changes were seen in PSG parameters when ABPM was co‐performed with PSG, including sleep efficiency and arousals. In total, 12 of the 41 patients were identified as having nocturnal hypertension. Our study is important in that it shows that concomitant use of ABPM during PSG can aid in the early identification of nocturnal hypertension in this population.
Synthesis of Some Novel Bis Type 2-Mercapto Benzimidazole Derivatives

The conventional methodology was adopted to synthesize the title compounds.The synthesis of titled compound from starting material i.e substituted 2-mercapto benzimidazoles was prepared from substituted ophenylenediamine and carbon disulphide in presence of KOH in single step, initially the substituted 2-mercapto benzimidazole compounds are subjected to S-acylation by treating with acetyl chloride in acetone in the presence of potassium carbonate, results formation of acylated compounds. Which are further treated with 1,2-dibromo ethane and 1,3-dibromo propane using potassium carbonate as deacidifying agent, to get their respective
Efficacy of UVC-treated, pathogen-reduced platelets versus untreated platelets: a randomized controlled non-inferiority trial

Pathogen reduction (PR) technologies for blood components have been established to reduce the residual risk of known and emerging infectious agents. THERAFLEX UV-Platelets, a novel ultraviolet C (UVC) light-based PR technology for platelet concentrates, works without photoactive substances. This randomized, controlled, double-blind, multicenter, non-inferiority trial was designed to compare the efficacy and safety of UVC-treated platelets to that of untreated platelets in thrombocytopenic patients with hematologic-oncologic diseases. The primary objective was to determine non-inferiority of UVC-treated platelets, assessed by the 1-hour corrected count increment (CCI) in up to eight per-protocol platelet transfusion episodes. Analysis of the 171 eligible patients showed that the defined non-inferiority margin of 30% of UVC-treated platelets was narrowly missed as the mean differences in 1-hour CCI between standard platelets versus UVC-treated platelets for intention-to-treat and per-protocol analyses were 18.2% (95% Confidence Interval [CI]: 6.4-30.1) and 18.7% (95% CI: 6.3-31.1), respectively. In comparison to the control, the UVC group had a 19.2% lower mean 24-hour CCI and was treated with an about 25% higher number of platelet units, but the average number of days to the next platelet transfusion did not differ significantly between both treatment groups. The frequency of low-grade adverse events was slightly higher in the UVC group and the frequencies of refractoriness to platelet transfusion, platelet alloimmunization, severe bleeding events, and red blood cell transfusions were comparable between groups. Our study suggests that transfusion of pathogen-reduced platelets produced with the UVC technology is safe but non-inferiority was not demonstrated. (clinicaltrials gov. Identifier: DRKS00011156).