Miracle-dz/UniFAR-FTUs huggingface dataset:
Facilitating reproducible project management and manuscript development in team science: The projects R package

The contemporary scientific community places a growing emphasis on the reproducibility of research. The projects R package is a free, open-source package created in the interest of facilitating reproducible research workflows. It adds to existing software tools for reproducible research and introduces several practical features that are helpful for scientists and their collaborative research teams. For each individual project, it supplies a framework for storing raw and cleaned study data sets, and it provides script templates for protocol creation, data cleaning, data analysis and manuscript development. Internal databases of project and author information are generated and displayed, and manuscript title pages containing author lists and their affiliations are automatically generated from the internal database. File management tools allow teams to organize multiple projects. When used on a shared file system, multiple researchers can harmoniously contribute to the same project in a less punctuated manner, reducing the frequency of misunderstandings and the need for status updates.
Relationship Between Diet, Tinnitus, and Hearing Difficulties

Supplemental Digital Content is available in the text. Objectives: Diet may affect susceptibility of the inner ear to noise and age-related effects that lead to tinnitus and hearing loss. This study used complementary single nutrient and dietary pattern analysis based on statistical grouping of usual dietary intake in a cross-sectional analysis of tinnitus and hearing difficulties in a large population study sample. Design: The research was conducted using the UK Biobank resource. Tinnitus was based on report of ringing or buzzing in one or both ears that lasts more than five minutes at a time and is currently experienced at least some of the time. Identification of a hearing problem was based on self-reported difficulties with hearing. Usual dietary intake and dietary patterns (involving statistical grouping of intake to account for how foods are combined in real-life diets) were estimated based on between two and five administrations of the Oxford Web-Q 24-hour dietary recall questionnaire over the course of a year for 34,576 UK adult participants aged 40 to 69. Results: In a multivariate model, higher intake of vitamin B12 was associated with reduced odds of tinnitus, while higher intakes of calcium, iron, and fat were associated with increased odds (B12, odds ratio [OR] 0.85, 95% confidence interval [CI] 0.75 to 0.97; Calcium, OR 1.20, 95% CI 1.08 to 1.34; Iron, OR 1.20, 95% CI 1.05 to 1.37; Fat, OR 1.33, 95% CI 1.09 to 1.62, respectively, for quintile 5 versus quintile 1). A dietary pattern characterised by high protein intake was associated with reduced odds of tinnitus (OR 0.90, 95% CI 0.82 to 0.99 for quintile 5 versus quintile 1). Higher vitamin D intake was associated with reduced odds of hearing difficulties (OR 0.90, 95% CI 0.81 to 1.00 for quintile 5 versus quintile 1), as were dietary patterns high in fruit and vegetables and meat and low in fat (Prudent diet: OR 0.89, 95% CI 0.83 to 0.96; High protein: OR 0.88, 95% CI 0.82 to 0.95; High fat: OR 1.16, 95% CI 1.08 to 1.24, respectively, for quintile 5 versus quintile 1). Conclusions: There were associations between both single nutrients and dietary patterns with tinnitus and hearing difficulties. Although the size of the associations was small, universal exposure for dietary factors indicates that there may be a substantial impact of diet on levels of tinnitus and hearing difficulties in the population. This study showed that dietary factors might be important for hearing health.
Progressive Supranuclear Palsy, Corticobasal Degeneration, and Multiple System Atrophy.

PURPOSE OF REVIEW Patients who have parkinsonian features, especially without tremor, that are not responsive to levodopa, usually have one of these three major neurodegenerative disorders rather than Parkinson disease: progressive supranuclear palsy (PSP), multiple system atrophy (MSA), or corticobasal degeneration (CBD). Each of these disorders eventually develops signs and symptoms that distinguish it from idiopathic Parkinson disease, but these may not be present at disease onset. Although these conditions are not generally treatable, it is still important to correctly diagnose the condition as soon as possible. RECENT FINDINGS In recent years, it has been increasingly recognized that the symptoms of these diseases do not accurately predict the pathology, and the pathology does not accurately predict the clinical syndrome. Despite this, interest has grown in treating these diseases by targeting misfolded tau (in the case of PSP and CBD) and misfolded α-synuclein (in the case of MSA). SUMMARY Knowledge of the characteristic signs and symptoms of PSP, MSA, and CBD are essential in diagnosing and managing patients who have atypical parkinsonian syndromes.
Dissecting macroecological and macroevolutionary patterns of forest biodiversity across the Hawaiian archipelago

Significance Integrating evolutionary and ecological factors is an essential step toward reaching a more complete understanding of the mechanisms underlying biodiversity patterns. While oceanic islands are often used as natural laboratories, typical analyses lack information about species abundances and distributions within islands that is necessary to disentangle the effects of biogeographical and ecological factors on biodiversity. We analyze forests across the Hawaiian archipelago and show that the effects of island age on diversity patterns of native species percolate across spatial scales via the distribution of rare species. However, we found that biological invasions are eroding the signal of island age on biodiversity. Overall, we show that diversity patterns across a biodiversity hotspot reflect the joint influence of contemporary and historical drivers. Biodiversity patterns emerge as a consequence of evolutionary and ecological processes. Their relative importance is frequently tested on model ecosystems such as oceanic islands that vary in both. However, the coarse-scale data typically used in biogeographic studies have limited inferential power to separate the effects of historical biogeographic factors (e.g., island age) from the effects of ecological ones (e.g., island area and habitat heterogeneity). Here, we describe local-scale biodiversity patterns of woody plants using a database of more than 500 forest plots from across the Hawaiian archipelago, where these volcanic islands differ in age by several million years. We show that, after controlling for factors such as island area and heterogeneity, the oldest islands (Kaua’i and O’ahu) have greater native species diversity per unit area than younger islands (Maui and Hawai’i), indicating an important role for macroevolutionary processes in driving not just whole-island differences in species diversity, but also local community assembly. Further, we find that older islands have a greater number of rare species that are more spatially clumped (i.e., higher within-island β-diversity) than younger islands. When we included alien species in our analyses, we found that the signal of macroevolutionary processes via island age was diluted. Our approach allows a more explicit test of the question of how macroevolutionary factors shape not just regional-scale biodiversity, but also local-scale community assembly patterns and processes in a model archipelago ecosystem, and it can be applied to disentangle biodiversity drivers in other systems.
Integration of Database Management System with Cloud

: In recent years, outsourcing the database has become an important component of cloud computing. Due to the continuous advancements in a network technology, the cost required to transmit a terabyte of data over long distances as decreased significantly in the past decade. In addition, the total cost of data management is five to ten times higher than the initial acquisition cost. As a result, there is a growing interest in outsourcing database management tasks to third parties that can provide these tasks for much lower cost due to the economy of scale. This new outsourcing model has the benefits of reducing the cost for running Database Management System (DBMS) independently.
Acute Demands and Recovery From Common Interval Training Protocols

Supplemental Digital Content is Available in the Text. Abstract Elmer, DJ, Barron, EN, and Chavez, JL. Acute demands and recovery from common interval training protocols. J Strength Cond Res 35(11): 3041–3049, 2021—The definition of interval training is quite broad, with no accepted procedure for classifying protocols with different workloads and work and recovery interval times. In addition, little is known about the differences in training load and recovery from common interval protocols. The purpose of this study was to evaluate the differences in acute physiological demands and perceived difficulty between 3 common interval training protocols and a moderate, continuous exercise session. Eight subjects completed the training sessions on a cycle ergometer in a randomized order, with at least 1 week between sessions: 30-second/4-minute, 1-minute/1-minute, 4-minute/3-minute, and a 45-minute continuous session. Metabolic variables were measured throughout exercise and 30 minutes of recovery. Training impulse (TRIMP), session-RPE, and RPE-training load were also measured. There were significant differences between protocols, including between interval training protocols, for average V̇o2 (p < 0.001) and heart rate (HR) (p = 0.02), total O2 consumption (p < 0.001), peak lactate (p < 0.001), TRIMP (p = 0.02), session-RPE (p = 0.01), and RPE-training load (p < 0.001). There were no significant differences between interval training protocols for peak V̇o2 or peak HR attained during exercise. There were also no differences in V̇o2 or HR after 5 or 30 minutes of recovery. Blood lactate was only significantly higher after 30 minutes of recovery from the 30-second/4-minute compared with the 4-minute/3-minute protocol (p = 0.001) and the 45-minute session (p < 0.001). These findings show a range of differences in acute physiological demands and perceptions from interval training protocols, which should be accounted for when planning training sessions or research studies or when interpreting past research.
A thylakoid membrane-bound and redox-active rubredoxin (RBD1) functions in de novo assembly and repair of photosystem II

Significance Photosystem II (PSII) catalyzes the light-driven oxidation of water in photosynthesis, supplying energy and oxygen to many life-forms on earth. During PSII assembly and repair, PSII intermediate complexes are prone to photooxidative damage, requiring mechanisms to minimize this damage. Here, we report the functional characterization of RBD1, a PSII assembly factor that interacts with PSII intermediate complexes to ensure their functional assembly and repair. We propose that the redox activity of RBD1 participates together with the cytochrome b559 to protect PSII from photooxidation. This work not only improves our understanding of cellular protection mechanisms for the vital PSII complex but also informs genetic engineering strategies for protection of PSII repair to increase agricultural productivity. Photosystem II (PSII) undergoes frequent photooxidative damage that, if not repaired, impairs photosynthetic activity and growth. How photosynthetic organisms protect vulnerable PSII intermediate complexes during de novo assembly and repair remains poorly understood. Here, we report the genetic and biochemical characterization of chloroplast-located rubredoxin 1 (RBD1), a PSII assembly factor containing a redox-active rubredoxin domain and a single C-terminal transmembrane α-helix (TMH) domain. RBD1 is an integral thylakoid membrane protein that is enriched in stroma lamellae fractions with the rubredoxin domain exposed on the stromal side. RBD1 also interacts with PSII intermediate complexes containing cytochrome b559. Complementation of the Chlamydomonas reinhardtii (hereafter Chlamydomonas) RBD1-deficient 2pac mutant with constructs encoding RBD1 protein truncations and site-directed mutations demonstrated that the TMH domain is essential for de novo PSII assembly, whereas the rubredoxin domain is involved in PSII repair. The rubredoxin domain exhibits a redox midpoint potential of +114 mV and is proficient in 1-electron transfers to a surrogate cytochrome c in vitro. Reduction of oxidized RBD1 is NADPH dependent and can be mediated by ferredoxin-NADP+ reductase (FNR) in vitro. We propose that RBD1 participates, together with the cytochrome b559, in the protection of PSII intermediate complexes from photooxidative damage during de novo assembly and repair. This role of RBD1 is consistent with its evolutionary conservation among photosynthetic organisms and the fact that it is essential in photosynthetic eukaryotes.
Measuring Communication Similarity Between Hospice Nurses and Cancer Caregivers Using Latent Semantic Analysis

Background Optimal end-of-life care requires effective communication between hospice nurses, caregivers, and patients, yet defining and evaluating effective communication are challenging. Latent semantic analysis (LSA) measures the degree of communication similarity (talking about the same topic) without relying on specific word choices or matching of communication behaviors (question-answer), thus more comprehensively evaluating communication interactions. Objective Guided by the Communication Accommodation Theory, we evaluated communication similarity, indicating theoretical convergence, between hospice nurses and caregivers of cancer patients, identifying nurse attributes and communication skills that were associated with greater communication similarity. Methods A descriptive secondary analysis of self-reported nurse data and 31 audio-recorded cancer patient home hospice nursing visits across 2 states and 7 hospices. Results The average LSA score was 0.83 (possible range, 0–1). A nurse preference for greater patient-oriented visits, use of more Nurse Partnering statements, and less Conversation Dominance (ratio of total nurse to total caregiver talk) were associated with higher LSA scores. Conclusions Effective communication is essential to optimal end-of-life care. Latent semantic analysis is a feasible and promising approach for assessing communication similarity during home hospice care. Implications for Practice Hospice nurses are at the forefront of family caregiver communication, playing a vital role in empowering caregivers to assume required patient care tasks. Communication strategies such as the use of partnering statements that increase LSA scores can be taught to hospice nurses and other members of the hospice interdisciplinary team as a way to enrich communication skills and improve communication confidence and can be translated into other oncology nursing contexts.
A Mini-Review: Clinical Development and Potential of Aptamers for Thrombotic Events Treatment and Monitoring

The unique opportunity for aptamer uses in thrombotic events has sparked a considerable amount of research in the area. The short half-lives of unmodified aptamers in vivo remain one of the major challenges in therapeutic aptamers. Much of the incremental successful therapeutic aptamer stories were due to modifications in the aptamer bases. This mini-review briefly summarizes the successes and challenges in the clinical development of aptamers for thrombotic events, and highlights some of the most recent developments in using aptamers for anticoagulation monitoring.
Change in left atrial function predicts incident atrial fibrillation: the Multi-Ethnic Study of Atherosclerosis

Abstract Aims Longitudinal change in left atrial (LA) structure and function could be helpful in predicting risk for incident atrial fibrillation (AF). We used cardiac magnetic resonance (CMR) imaging to explore the relationship between change in LA structure and function and incident AF in a multi-ethnic population free of clinical cardiovascular disease at baseline. Methods and results In the Multi-Ethnic Study of Atherosclerosis (MESA), 2338 participants, free at baseline of clinically recognized AF and cardiovascular disease, had LA volume and function assessed with CMR imaging, at baseline (2000–02), and at Exam 4 (2005–07) or 5 (2010–12). Free of AF, 124 participants developed AF over 3.8 ± 0.9 years (2015) following the second imaging. In adjusted Cox regression models, an average annualized change in all LA parameters were significantly associated with an increased risk of AF. An annual decrease of 1-SD unit in total LA emptying fractions (LAEF) was most strongly associated with risk of AF after adjusting for clinical risk factors for AF, baseline LA parameters, and left ventricular mass-to-volume ratio (hazard ratio per SD = 1.91, 95% confidence interval = 1.53–2.38, P < 0.001). The addition of change in total LAEF to an AF risk score improved model discrimination and reclassification (net reclassification improvement = 0.107, P = 0.017; integrative discrimination index = 0.049, P < 0.001). Conclusion In this multi-ethnic study population free of clinical cardiovascular disease at baseline, a greater increase in LA volumes and decrease in LA function were associated with incident AF. The addition of change in total LAEF to risk prediction models for AF improved model discrimination and reclassification of AF risk.
Diminished Condensin Gene Expression Drives Chromosome Instability That May Contribute to Colorectal Cancer Pathogenesis

Chromosome instability (CIN), or constantly evolving chromosome complements, is a form of genome instability implicated in the development and progression of many cancer types, however, the molecular determinants of CIN remain poorly understood. Condensin is a protein complex involved in chromosome compaction, and recent studies in model organisms show that aberrant compaction adversely impacts mitotic fidelity. To systematically assess the clinical and fundamental impacts that reduced condensin gene expression have in cancer, we first assessed gene copy number alterations of all eight condensin genes. Using patient derived datasets, we show that shallow/deep deletions occur frequently in 12 common cancer types. Furthermore, we show that reduced expression of each gene is associated with worse overall survival in colorectal cancer patients. To determine the overall impact that reduced condensin gene expression has on CIN, a comprehensive siRNA-based screen was performed in two karyotypically stable cell lines. Following gene silencing, quantitative imaging microscopy identified increases in CIN-associated phenotypes, including changes in nuclear areas, micronucleus formation, and chromosome numbers. Although silencing corresponded with increases in CIN phenotypes, the most pronounced phenotypes were observed following SMC2 and SMC4 silencing. Collectively, our clinical and fundamental findings suggest reduced condensin expression and function may be a significant, yet, underappreciated driver of colorectal cancer.
Severe cases of seasonal influenza in Russia in 2017-2018

The 2017–2018 influenza epidemic season in Russia was characterized by a relatively low morbidity and mortality. We evaluated herd immunity prior to the 2017–2018 influenza season in hemagglutination inhibition assay, and performed characterization of influenza viruses isolated from severe or fatal influenza cases and from influenza cases in people vaccinated in the fall of 2017. During the 2017–2018 epidemic season, 87 influenza A and B viruses were isolated and viruses of the 75 influenza cases, including selected viral isolates and viruses analyzed directly from the original clinical material, were genetically characterized. The analyzed A(H1N1)pdm09 viruses belonged to clade 6B.1, B/Yamagata-like viruses belonged to clade 3, and B/Victoria-like viruses belonged to clade 1A and they were antigenically similar to the corresponding vaccine strains. A(H3N2) viruses belonged to clade 3C.2a and were difficult to characterize antigenically and the analysis indicated antigenic differences from the corresponding egg-grown vaccine strain. The next generation sequencing revealed the presence of D222/G/N polymorphism in the hemagglutinin gene in 32% of the analyzed A(H1N1)pdm09 lethal cases. This study demonstrated the importance of monitoring D222G/N polymorphism, including detection of minor viral variants with the mutations, in the hemagglutinin gene of A(H1N1)pdm09 for epidemiological surveillance. One strain of influenza virus A(H1N1)pdm09 was resistant to oseltamivir and had the H275Y amino acid substitution in the NA protein. All other isolates were susceptible to NA inhibitors. Prior to the 2017–2018 epidemic season, 67.4 million people were vaccinated, which accounted for 46.6% of the country's population. Just before the epidemic season 33–47% and 24–30% of blood sera samples collected within the territory of Russia showed the presence of protective antibody titers against vaccine strains of influenza A and influenza B/Victoria-like, respectively. Mass vaccination of the population had evidently reduced the severity of the flu epidemic during the 2017–2018 influenza epidemic season in Russia.
The algebraic Atiyah-Hirzebruch spectral sequence of real projective spectra

In this note, we use Curtis's algorithm and the Lambda algebra to compute the algebraic Atiyah-Hirzebruch spectral sequence of the suspension spectrum of $\mathbb{R}P^\infty$ with the aid of a computer, which gives us its Adams $E_2$-page in the range of $t<72$. We also compute the transfer map on the Adams $E_2$-pages. These data are used in our computations of the stable homotopy groups of $\mathbb{R}P^\infty$ in [6] and of the stable homotopy groups of spheres in [7].
Sustained Release Strategy Designed for Lixisenatide Delivery to Synchronously Treat Diabetes and Associated Complications.

Diabetes and its complications have become a global challenge of public health. Herein, we aimed to develop a long-acting delivery system of lixisenatide (Lixi), a glucose-dependent antidiabetic peptide, based on an injectable hydrogel for the synchronous treatment of type 2 diabetic mellitus (T2DM) and associated complications. Two triblock copolymers, poly(ε-caprolactone-co-glycolic acid)-poly(ethylene glycol)-poly(ε-caprolactone-co-glycolic acid) (PCGA-PEG-PCGA) and poly(D, L-lactic acid-co-glycolic acid)-poly(ethylene glycol)-poly(D, L-lactic acid-co-glycolic acid) (PLGA-PEG-PLGA) possessing temperature-induced sol-gel transitions, were synthesized by us. Compared to the two single-component hydrogels, their 1/1 mixture hydrogel not only maintained the temperature-induced gelation but also exhibited a steadier degradation profile in vivo. Both in vitro and in vivo release studies demonstrated that the mixture hydrogel provided the sustained release of Lixi for up to 9 days, which was attributed to balanced electrostatic interactions between the positive charges in the peptide and the negative charges in the polymer carrier. The hypoglycemic efficacy of Lixi delivered from the mixture hydrogel after a single subcutaneous injection into diabetic db/db mice was comparable to that of twice-daily administrations of Lixi solution for up to 9 days. Furthermore, three successive administrations of the abovementioned gel system within a month significantly increased the plasma insulin level, lowered glycosylated hemoglobin and improved the pancreatic function of the animals. These results were superior or equivalent to those of twice-daily injections of Lixi solution for 30 days, but the number of injections was markedly reduced from 60 to 3. Finally, an improvement in hyperlipidemia, augmentation of nerve fiber density and enhancement of motor nerve conduction velocity in the gel formulation-treated db/db mice indicated that the sustained delivery of Lixi arrested and even ameliorated diabetic complications. These findings suggested that the Lixi-loaded mixture hydrogel has great potential for the treatment of T2DM with significant improvements in the health and quality of life of patients.