Miracle-dz/UniFAR-FTUs huggingface dataset:
Examining implementation and effects of a comprehensive community intervention addressing type 2 diabetes among high-risk minority patients in Durham County, NC

Abstract Type-2 diabetes affects millions of people. Racial minorities are at higher risk for developing diabetes and suffering complications. Duke University and its partners built a team to improve population-level health outcomes and reduce health disparities in Durham County, NC. An empirical case study design was used to examine the Durham Diabetes Program (DDP) and its effects on emergency department (ED) visits and hospital admissions (HAs). High-risk program participants (N = 200) were enrolled into the DDP using a risk algorithm. Culturally competent teams delivered various intervention components that were anchored in behavior change strategies (e.g. diabetes self-management education and support, enhancing clinical care, community mobilization, and health system/community transformation). More than a hundred community/system changes were implemented as part of the DDP. Further, the DDP was associated with decreased ED visits (by 34%) and HAs (by 40.5%). This research can inform the way diabetes is assessed and interventions are delivered.
Post-Operative Blood Salvage and Autotransfusion for Adult Spinal Deformity: A Randomized Controlled Trial.

STUDY DESIGN Randomized controlled trial. OBJECTIVE To determine whether post-operative blood salvage and autotransfusion vs. traditional closed suction drainage reduces the rate of homologous blood transfusions in patients undergoing surgery for adult spinal deformity. SUMMARY OF BACKGROUND DATA The use of intra-operative blood salvage has become commonplace in spine surgery; however, the collection and reinfusion of blood drained from the wound post-operatively has not been employed routinely due to increased cost and questionable benefit. METHODS Adult patients undergoing long posterior fusions were randomized to either a blood salvage and reinfusion system (OrthoPat - Group 1) or a standard subfascial closed suction drain (Group 2). Blood collected in Group 1 was reinfused according to the manufacturer's protocol. Reinfusion drains were converted to standard closed suction drains when output was less than 50cc over 4 hours, and drains were removed when output was minimal. Patients received autologous or homologous blood transfusions when Hg < 8 g/dL or they had symptomatic anemia. RESULTS 34 patients were randomized into Group 1 and 36 patients into Group 2. There were no differences in pre-operative or intra-operative parameters. Patients in Group 1 had higher hemoglobin levels on POD #2 and POD #3 compared to those in Group 2. However, there was no significant difference in the percentage of patients requiring homologous blood transfusion between the two groups (41% Group 1 vs. 60% Group 2, p = 0.17). Similarly a subgroup analysis in patients with EBL > 2000cc also showed no difference in homologous blood transfusion rates (67% Group 1 vs. 76% Group 2, p = 0.58). There were no differences in the rate or type of post-operative complications. CONCLUSIONS Post-operative blood salvage and reinfusion results in a higher hemoglobin level in the early post-operative period, but does not significantly reduce the need for homologous blood transfusion. LEVEL OF EVIDENCE 1.
Variations in Surgical Procedures for Inducing Hind Limb Ischemia in Mice and the Impact of These Variations on Neovascularization Assessment

Mouse hind limb ischemia is the most common used preclinical model for peripheral arterial disease and critical limb ischemia. This model is used to investigate the mechanisms of neovascularization and to develop new therapeutic agents. The literature shows many variations in the model, including the method of occlusion, the number of occlusions, and the position at which the occlusions are made to induce hind limb ischemia. Furthermore, predefined end points and the histopathological and radiological analysis vary. These differences hamper the correlation of results between different studies. In this review, variations in surgical methods of inducing hind limb ischemia in mice are described, and the consequences of these variations on perfusion restoration and vascular remodeling are discussed. This study aims at providing the reader with a comprehensive overview of the methods so far described, and proposing uniformity in research of hind limb ischemia in a mouse model.
Steric microstructure of mixed-species biofilm formed by interaction between Lactobacillus plantarum ML11-11 and Saccharomyces cerevisiae

ABSTRACT The mixed-species biofilm of Lactobacillus plantarum ML11-11 (LAB) and yeast had a double-layered structure with the ground layer composed of LAB cells, and the upper layer composed of coaggregates of LAB and yeast cells. The ability of LAB to adhere to both, the solid surface and the yeast cells, enabled the formation and maintenance of the biofilm as an ecosystem for LAB and yeast.
Environmental Toxicology and Chemistry

Studies of the South Saskatchewan River confirmed that N,N‐diethyl‐m‐toluamide (DEET) is ubiquitous at 10 to 20 ng/L, whereas in effluent‐dominated Wascana Creek, levels of 100 to 450 ng/L were observed. Effects of DEET exposure were assessed in microbial communities using a wide variety of measures. Communities developed in rotating annular reactors with either 100 or 500 ng/L DEET, verified using gas chromatography‐mass spectrometry analyses. Microscale analyses indicated that both DEET concentrations resulted in significant (p < 0.05) declines in photosynthetic biomass, whereas bacterial biomass was unaffected. There was no detectable effect of DEET on the levels of chlorophyll a. However, pigment analyses indicated substantial shifts in algal–cyanobacterial community structure, with reductions of green algae and some cyanobacterial groups at 500 ng/L DEET. Protozoan/micrometazoan grazers increased in communities exposed to 500 ng/L, but not 100 ng/L, DEET. Based on thymidine incorporation or utilization of carbon sources, DEET had no significant effects on metabolic activities. Fluorescent lectin‐binding analyses showed significant (p < 0.05) changes in glycoconjugate composition at both DEET concentrations, consistent with altered community structure. Principal component cluster analyses of denaturing gradient gel electrophoresis indicated that DEET exposure at either concentration significantly changed the bacterial community (p < 0.05). Analyses based on 16S ribosomal RNA of community composition confirmed changes with DEET exposure, increasing detectable beta‐proteobacteria, whereas actinobacteria and acidimicrobia became undetectable. Further, cyanobacteria in the subclass Oscillatoriophycideae were similarly not detected. Thus, DEET can alter microbial community structure and function, supporting the need for further evaluation of its effects in aquatic habitats. Environ Toxicol Chem 2019;38:2414–2425. © 2019 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals, Inc. on behalf of SETAC.
A Phase-Preserving Focusing Technique for TOPS Mode SAR Raw Data Based on Conventional Processing Methods

We present a new solution for the phase-preserving focusing of synthetic aperture radar (SAR) raw data acquired through the Terrain Observation with Progressive Scan (TOPS) mode. The proposed algorithm consists of a first interpolation stage of the TOPS raw data, which takes into account the Doppler Centroid frequency variations due to the azimuth antenna steering function, and allows us to unfold the azimuth spectra of the TOPS raw data. Subsequently, the interpolated signals are processed by using conventional phase-preserving SAR focusing methods that exploit frequency domain and spectral analyses algorithms, which are extensively used to efficiently process Stripmap and ScanSAR data. Accordingly, the developed focusing approach is easy to implement. In particular, the presented focusing approach exploits one of the available frequency domain Stripmap processing techniques. The only modification is represented by the inclusion, within the 2D frequency domain focusing step, of a spurious azimuth chirp signal with a properly selected azimuthal rate. This allows us to efficiently carry out the TOPS azimuth focusing through the SPECAN method. Furthermore, an important aspect of this algorithm is the possibility to easily achieve a constant and tunable output azimuth pixel size without any additional computing time; this is a remarkable feature with respect to the full-aperture TOPS-mode algorithms available in the existing literature. Moreover, although tailored on Sentinel-1 (S1) raw data, the proposed algorithm can be easily extended to process data collected through the TOPS mode by different radar sensors. The presented experimental results have been obtained by processing real Sentinel-1 raw data and confirm the effectiveness of the proposed algorithm.
Evaluation of model refinement in CASP13

Performance in the model refinement category of the 13th round of Critical Assessment of Structure Prediction (CASP13) is assessed, showing that some groups consistently improve most starting models whereas the majority of participants continue to degrade the starting model on average. Using the ranking formula developed for CASP12, it is shown that only 7 of 32 groups perform better than a “naïve predictor” who just submits the starting model. Common features in their approaches include a dependence on physics‐based force fields to judge alternative conformations and the use of molecular dynamics to relax models to local minima, usually with some restraints to prevent excessively large movements. In addition to the traditional CASP metrics that focus largely on the quality of the overall fold, alternative metrics are evaluated, including comparisons of the main‐chain and side‐chain torsion angles, and the utility of the models for solving crystal structures by the molecular replacement method. It is proposed that the introduction of these metrics, as well as consideration of the accuracy of coordinate error estimates, would improve the discrimination between good and very good models.
Expression of Normally Repressed Myosin Heavy Chain 7b in the Mammalian Heart Induces Dilated Cardiomyopathy

Background In mammals, muscle contraction is controlled by a family of 10 sarcomeric myosin motors. The expression of one of its members, MYH7b, is regulated by alternative splicing, and while the protein is restricted to specialized muscles such as extraocular muscles or muscle spindles, RNA that cannot encode protein is expressed in most skeletal muscles and in the heart. Remarkably, birds and snakes express MYH7b protein in both heart and skeletal muscles. This observation suggests that in the mammalian heart, the motor activity of MYH7b may only be needed during development since its expression is prevented in adult tissue, possibly because it could promote disease by unbalancing myocardial contractility. Methods and Results We have analyzed MYH7b null mice to determine the potential role of MYH7b during cardiac development and also generated transgenic mice with cardiac myocyte expression of MYH7b protein to measure its impact on cardiomyocyte function and contractility. We found that MYH7b null mice are born at expected Mendelian ratios and do not have a baseline cardiac phenotype as adults. In contrast, transgenic cardiac MYH7b protein expression induced early cardiac dilation in males with significantly increased left ventricular mass in both sexes. Cardiac dilation is progressive, leading to early cardiac dysfunction in males, but later dysfunction in females. Conclusions The data presented show that the expression of MYH7b protein in the mammalian heart has been inhibited during the evolution of mammals most likely to prevent the development of a severe cardiomyopathy that is sexually dimorphic.
Outcomes and clinical characteristics of transmural intestinal necrosis in acute mesenteric ischemia

Abstract Background: Acute mesenteric ischemia (AMI) is a rare life-threatening condition, especially for the patients with transmural intestinal necrosis (TIN). However, the optimal time for surgical intervention is controversial. As a series study, this study aimed to identify the outcomes and clinical characteristic of patients with TIN. Methods: Clinical data of 158 patients with AMI from January 2010 to December 2017 were retrospectively analyzed in a national gastrointestinal referral center in China to confirm the outcomes and identify predictors for TIN. Results: According to the results of pathological assessment and follow-up, 62 patients were TIN and 96 were non-TIN. Patients with TIN have a higher mortality and incidence of severe complications. The significant independent predictors for TIN were arterial lactate level (OR: 4.76 [2.29 ∼ 9.89]), free intraperitoneal fluid (OR: 9.49 [2.56 ∼ 35.24]) and pneumatosis intestinalis (OR: 7.08 [1.68 ∼ 29.82]) in computed tomography (CT) scan imaging. The overall area under the receiver operating characteristics (ROC) curve of the model was 0.934 (95% confidence interval: 0.893 ∼ 0.974). Using ROC curve, the cutoff value of arterial lactate level predicting the onset of TIN was 2.65 mmol/L. Conclusions: Patients concomitant with TIN manifest a higher risk of poor prognosis. The three predictors for TIN were arterial lactate level >2.65 mmol/L, free intraperitoneal fluid and pneumatosis intestinalis. Close monitoring these predictors would help identify AMI patients developed TIN and in urgent need for bowel resection.
HDL-C Role in Acquired Aortic Valve Stenosis Patients and Its Relationship with Oxidative Stress

Background and objectives: Mechanical stress is currently considered as the main factor promoting calcific aortic valve stenosis (AS) onset. It causes endothelial damage and dysfunction. The chronic inflammatory process causes oxidative stress. Oxidative stress-induced high-density lipoprotein cholesterol (HDL-C) dysfunction is an important component of the development of AS. The aim of the study was to evaluate the role of HDL-C in AS patients in three severity grades and in relation to the biomarkers of oxidative stress, thioredoxin reductase 1 (TrxR1) and myeloperoxidase (MPO). Materials and Methods: 18 patients with mild, 19 with moderate. and 15 with severe AS were included in the study, and 50 individuals were enrolled in the control group. Stenosis severity was determined by echocardiography. The TrxR1 and MPO were analyzed by ELISA, and HDL-C by commercially available tests. Data were analyzed using GraphPad Prism 8. Results: HDL-C in AS patients vs. control substantially decreases and this decline was observed in all three AS severity groups: mild (p = 0.018), moderate (p = 0.0002), and severe (p = 0.004). In both the control and the stenosis group, the HDL-C was higher in women than in men. In comparison to control, the HDL-C level was lower in the AS group, and more pronounced in women (p = 0.0001) than in men (p = 0.049). A higher TrxR1 level was observed in patients with mild (p = 0.0001) and severe AS (p = 0.047). However, a clear correlation between TrxR1 and HDL-C was not obtained. Analysis of MPO showed differences in all severity grades vs. control (p = 0.024 mild stenosis; p = 0.002 moderate stenosis; p = 0.0015 severe stenosis). A negative correlation (p = 0.047; rp = −0.28) was found between MPO and HDL-C, which confirms the adverse effects of MPO resulting in HDL-C dysfunction. Conclusions: In this study, we justified HDL-C level association with AS development process. The results unequivocally substantiated the association between HDL-C and AS in all severity grades in women, but only in moderate AS for men, which we explained by the small number of men in the groups. The obtained correlation between the HDL-C and MPO levels, as well as the concurrent decrease in the HDL-C level and increase in the TrxR1 level, indicate in general an HDL-C association with oxidative stress in AS patients.
Decellularized liver transplant could be recellularized in rat partial hepatectomy model.

In situ recellularization of the liver decellularized scaffold is a potential therapeutic alternative for liver transplantation. We aimed to develop an in situ procedure for recellularization of the rat liver using sodium lauryl ether sulfate (SLES) compared with Triton X-100/SDS. Rat liver specimens were rinsed with PBS, decellularized with either Triton X-100/SDS or SLES, and finally rinsed by distilled water. The efficiency of decellularized liver scaffolds was evaluated by histological, confocal Raman microscopy, histochemical staining and DNA quantification assessments. Finally, in vivo studies were done to assess the biocompatibility of the liver scaffold by serum biochemical parameters and the recellularization capacity by histological and immunohistochemistry staining. Findings confirmed the preservation of extracellular matrix (ECM) components such as reticular, collagen, glycosaminoglycans and neutral carbohydrates in both Triton X-100/SDS- and SLES-treated livers. Hoechst, feulgen, Haematoxylin and eosin and DNA quantification assessments confirmed complete genetic content removal. The serological parameters showed no adverse impact on the liver functions. Transplantation of SLES-treated cell-free decellularized liver showed extensive neovascularization along with migration of the fibrocytes and adipocytes and some immune cells. Also, immunohistochemical staining showed that the oval cells, stellate cells, cholangiocytes and hepatocytes invaded extensively into the graft. It is concluded that SLES can be considered as a promising alternative in the liver decellularization process, and the transplanted decellularized liver can appropriately be revascularized and regenerated.
Probing the 3D architecture of the plant nucleus with microscopy approaches: challenges and solutions

ABSTRACT The eukaryotic cell nucleus is a central organelle whose architecture determines genome function at multiple levels. Deciphering nuclear organizing principles influencing cellular responses and identity is a timely challenge. Despite many similarities between plant and animal nuclei, plant nuclei present intriguing specificities. Complementary to molecular and biochemical approaches, 3D microscopy is indispensable for resolving nuclear architecture. However, novel solutions are required for capturing cell-specific, sub-nuclear and dynamic processes. We provide a pointer for utilising high-to-super-resolution microscopy and image processing to probe plant nuclear architecture in 3D at the best possible spatial and temporal resolution and at quantitative and cell-specific levels. High-end imaging and image-processing solutions allow the community now to transcend conventional practices and benefit from continuously improving approaches. These promise to deliver a comprehensive, 3D view of plant nuclear architecture and to capture spatial dynamics of the nuclear compartment in relation to cellular states and responses. Abbreviations: 3D and 4D: Three and Four dimensional; AI: Artificial Intelligence; ant: antipodal nuclei (ant); CLSM: Confocal Laser Scanning Microscopy; CTs: Chromosome Territories; DL: Deep Learning; DLIm: Dynamic Live Imaging; ecn: egg nucleus; FACS: Fluorescence-Activated Cell Sorting; FISH: Fluorescent In Situ Hybridization; FP: Fluorescent Proteins (GFP, RFP, CFP, YFP, mCherry); FRAP: Fluorescence Recovery After Photobleaching; GPU: Graphics Processing Unit; KEEs: KNOT Engaged Elements; INTACT: Isolation of Nuclei TAgged in specific Cell Types; LADs: Lamin-Associated Domains; ML: Machine Learning; NA: Numerical Aperture; NADs: Nucleolar Associated Domains; PALM: Photo-Activated Localization Microscopy; Pixel: Picture element; pn: polar nuclei; PSF: Point Spread Function; RHF: Relative Heterochromatin Fraction; SIM: Structured Illumination Microscopy; SLIm: Static Live Imaging; SMC: Spore Mother Cell; SNR: Signal to Noise Ratio; SRM: Super-Resolution Microscopy; STED: STimulated Emission Depletion; STORM: STochastic Optical Reconstruction Microscopy; syn: synergid nuclei; TADs: Topologically Associating Domains; Voxel: Volumetric pixel
Long-Term Outcome of Anterior Cervical Decompression with Fusion for Cervical Ossification of Posterior Longitudinal Ligament including Postsurgical Remnant Ossified Spinal Lesion.

STUDY DESIGN A retrospective study OBJECTIVE. : To assess the outcome, perioperative complications, and prognostic factors of anterior cervical decompression and fusion (ACDF) in patients with cervical ossification of longitudinal ligament (OPLL). SUMMARY OF BACKGROUND DATA There is little information on the long-term surgical outcome of ACDF including postsurgical remnant ossified spinal lesion. METHODS Between 1993 and 2013, 80 patients with cervical myelopathy due to OPLL underwent ACDF at our hospital. Among these, 42 patients were followed-up for at least 5 years and their data were analyzed. RESULTS The mean follow-up period was 7.9 ± 2.8 years, and the overall improvement rate was 59.2 ± 15.0%. Although 12 (15.0%) perioperative complications were observed in 6 patients, accompanied by neurological deterioration, none of the patients had chronic complications. Multivariate logistic regression analysis that included the preoperative Japanese Orthopaedic Association (JOA) score, type of OPLL, occupying ratio of OPLL, and number of fused segments and increase in the transverse area of the cord identified the latter parameter as the only independent and significant determinant of radiological and clinical improvement of >50%. Among the patients with remaining ossified spinal lesions out of the decompressed range (16 patients), postoperative progression was observed in 6 cases (14.3%) who were all of the mixed type; floated lesions within the decompressed range did not show progression during the follow-up. Adjacent segment degeneration was seen in 9 (21.4%) patients, and neurological signs and symptoms were seen in only 3 of the 9 patients and only 1 patient required revision surgery. CONCLUSION The long-term clinical outcome of patients with cervical OPLL after ACDF is considered satisfactory. Surgery-related complications and adjacent segment diseases should not be reasons to avoid ACDF. Care should be taken in selecting ACDF with postsurgical remnant ossified spinal lesion since it could progress postoperatively especially in the mixed type OPLL. LEVEL OF EVIDENCE 4.
AAV9-Stathmin1 gene delivery improves disease phenotype in an intermediate mouse model of Spinal Muscular Atrophy.

Spinal muscular atrophy (SMA) is a devastating infantile genetic disorder caused by the loss of survival motor neuron (SMN) protein that leads to premature death due to loss of motor neurons and muscle atrophy. The approval of an antisense oligonucleotide (ASO) therapy for SMA was an important milestone in SMA research, however, effective next generation therapeutics will likely require combinatorial SMN-dependent therapeutics and SMN-independent disease modifiers. A recent cross-disease transcriptomic analysis identified Stathmin-1 (STMN1), a tubulin depolymerizing protein, as a potential disease modifier across different motor neuron diseases, including SMA. Here, we investigated whether viral-based delivery of STMN1 decreased disease severity in a well-characterized SMA mouse model. Intracerebroventricular delivery of scAAV9-STMN1 in SMA mice at P2 significantly increased survival and weight gain compared to untreated SMA mice without elevating Smn levels. scAAV9-STMN1 improved important hallmarks of disease, including motor function, NMJ pathology, and motor neuron cell preservation. Furthermore, scAAV9-STMN1 treatment restored microtubule networks and tubulin expression without affecting tubulin stability. Our results show that scAAV9-STMN1 treatment improves SMA pathology possibly by increasing microtubule turnover leading to restored levels of stable microtubules. Overall, these data demonstrate that STMN1 can significantly reduce the SMA phenotype independent of restoring SMN protein and highlight the importance of developing SMN-independent therapeutics for the treatment of SMA.