Miracle-dz/UniFAR-FTUs huggingface dataset:
Walking While Dialyzing: A Retrospective Observation of Early Mobility and Ambulation for Patients on Continuous Renal Replacement Therapy

Objectives: To describe the practice of physical therapy for patients requiring continuous renal replacement therapy and assess data related to the safety and feasibility of physical therapy interventions. Design: A retrospective observational cohort study. Patients: Surgical and cardiovascular patients receiving continuous renal replacement therapy during a 2-year period from December 2016 to November 2018. Setting: Two ICUs at a single academic medical center. Intervention: Physical mobility and ambulation while on continuous renal replacement therapy. Measurements and Main Results: Therapy data including ICU Mobility Scale score, number of physical therapy sessions with and without ambulation and gait distance, along with safety data including filter life, safety events, and mortality were analyzed. The cohort of patients receiving continuous renal replacement therapy during the 2-year period was 206. Of these, 172 (83.49%) received simultaneous physical therapy. The median ICU Mobility Scale was 5 (interquartile range, 4–7) over a total of 1,517 physical therapy sessions. Ambulation with concomitant continuous renal replacement therapy connected was achieved in 78 patients (37.86%). There were 377 ambulation sessions (24.85% of all sessions) with a mean of 4.83 (sds 4.94) ambulation sessions per ambulatory patient. Patients walked an average of 888.53 feet (sd 1,365.50) while on continuous renal replacement therapy and a daily average of 150.61 feet (sd 133.50). In-hospital mortality was lowest for patients who ambulated (17.95%) and highest for patients who received no therapy (73.53%). Continuous renal replacement therapy filter life was longest for patients who ambulated (2,047.20 min [sd 1,086.50 min]), and shortest in patients who received no therapy (1,682.20 min [sd 1,343.80 min]). One safety event was reported during this time (0.0007% of all physical therapy sessions). Conclusions: Ambulation while on continuous renal replacement therapy was not associated with an increased risk of safety events and was feasible with the use of nonfemoral catheters and dialysis equipment with internal batteries.
Tansley Review No. 71 Effects of elevated atmospheric CO2on woody plants

summary Because of their prominent role in the global carbon balance and their possible carbon sequestration, trees are very important organisms in relation to global climatic changes. Knowledge of these processes is the key to understanding the functioning of the whole forest ecosystem which can he modelled and predicted based on the physiological process information. This paper reviews the major methods and techniques used to examine the likely effects of elevated CO2 on woody plants, as well as the major physiological responses of trees to elevated CO2. The available exposure techniques and approaches are described. An overview table with all relevant literature data over the period 1989-93 summarizes the percent changes in biomass, root/shoot ratio, photosynthesis, leaf area and water use efficiency under elevated CO2. Interaction between growth, photosynthesis and nutrition is discussed with a special emphasis on downward regulation of photosynthesis. The stimulation or reduction found in the respiratory processes of woody plants are reviewed, as well as the effect of elevated CO2 on stomatal density, conductance and water use efficiency. Changes in plant quality and their consequences are examined. Changes in underground processes under elevated CO2 are especially emphasized and related to the functioning of the ecosystem. Some directions for future research are put forward.
Methylation Data Processing Protocol and Comparison of Blood and Cerebral Spinal Fluid Following Aneurysmal Subarachnoid Hemorrhage

One challenge in conducting DNA methylation-based epigenome-wide association study (EWAS) is the appropriate cleaning and quality-checking of data to minimize biases and experimental artifacts, while simultaneously retaining potential biological signals. These issues are compounded in studies that include multiple tissue types, and/or tissues for which reference data are unavailable to assist in adjusting for cell-type mixture, for example cerebral spinal fluid (CSF). For our study that evaluated blood and CSF taken from aneurysmal subarachnoid hemorrhage (aSAH) patients, we developed a protocol to clean and quality-check genome-wide methylation levels and compared the methylomic profiles of the two tissues to determine whether blood is a suitable surrogate for CSF. CSF samples were collected from 279 aSAH patients longitudinally during the first 14 days of hospitalization, and a subset of 88 of these patients also provided blood samples within the first 2 days. Quality control (QC) procedures included identification and exclusion of poor performing samples and low-quality probes, functional normalization, and correction for cell-type heterogeneity via surrogate variable analysis (SVA). Significant differences in rates of poor sample performance was observed between blood (1.1% failing QC) and CSF (9.12% failing QC; p = 0.003). Functional normalization increased the concordance of methylation values among technical replicates in both CSF and blood. SVA improved the asymptotic behavior of the test of association in a simulated EWAS under the null hypothesis. To determine the suitability of blood as a surrogate for CSF, we calculated the correlations of adjusted methylation values at each CpG between blood and CSF globally and by genomic regions. Overall, mean within-CpG correlation was low (r < 0.26), suggesting that blood is not a suitable surrogate for global methylation in CSF. However, differences in the magnitude of the correlation were observed by genomic region (CpG island, shore, shelf, open sea; p < 0.001 for all) and orientation with respect to nearby genes (3′ UTR, transcription start site, exon, body, 5′ UTR; p < 0.01 for all). In conclusion, the correlation analysis and QC pipelines indicated that DNA extracted from blood was not, overall, a suitable surrogate for DNA from CSF in aSAH methylomic studies.
Processing Code-Switches in the Presence of Others: An ERP Study

Code-switching is highly socially constrained. For instance, code-switching is only felicitous when those present are fluent in both languages. This means that bilinguals need to dynamically adjust their language control and expectation of code-switching to the current social situation or context. The aim of the present EEG study was to investigate how and when language control in the comprehension of code-switches is affected by the assumed language knowledge of others in the context. Spanish-English bilinguals read sentences with and without code-switches together with another Spanish-English bilingual or with an English monolingual. Switches elicited an early fronto-central positivity. This effect was smaller overall when a bilingual was present at the start of the study. In addition, the late positive complex found for switches was smaller when a bilingual was present rather than a monolingual, but only for those participants who were sensitive to the other’s language knowledge in their off-line judgments. These findings suggest that the bilinguals in our study expected and activated both languages when initially paired with a bilingual and that they more easily accommodated code-switches, in the presence of a bilingual than in the presence of a monolingual. Our findings support the view that language control can be modulated by the perceived language knowledge of others present, and are compatible with a dynamic control model of bilingual language comprehension.
Avian Egg Timers: Female Cowbirds Judge Past, Present, and Future When Making Nest Parasitism Decisions

The cognitive demands associated with brood parasitism are substantial. Not only must female parasites locate nests and assess their suitability for parasitism, they must also time parasitism to correspond with the breeding behavior of the host. Keeping track of the reproductive state of hosts for a variety of nests allows the parasite to select a nest where their egg can be incubated successfully. Thus, nest selection decisions are integral to obligate brood parasites’ reproductive success. In captive breeding flocks of brown-headed cowbirds (Molothrus ater), I provided females access to mock nests that varied in the number of eggs present. By changing the number of eggs added to nests across days, I studied (1) females’ abilities to time a host nest’s readiness for parasitism and (2) the timing of females’ nest selection decisions. I found that cowbirds can attend to the amount of time that elapsed since a host egg was added to a nest and can use that information to choose a nest for parasitism. Females made their choice of nest during prospecting the day before they laid, and, once decided, they did not update their decisions on the day of laying. Taken together, the results reveal that female cowbirds process substantial amounts of information about location, time, number, and rate in order to plan for future parasitism. This research program reveals that species-typical decisions integrate a variety of general and specialized cognitive abilities to allow females to behave adaptively and maximize reproductive success.
Serum-Free Medium Enhances the Therapeutic Effects of Umbilical Cord Mesenchymal Stromal Cells on a Murine Model for Acute Colitis

The usage of animal serum may ultimately prevent the application of ex vivo cultured mesenchymal stromal cells (MSCs) in a clinical setting due to safety concerns and batch-to-batch variability. Increasing regulatory pressure to limit use of animal serum has been issued and serum-free, xeno-free, and chemically defined media (S&XFM-CD) is encouraged to replace serum-containing media (SCM) in the stem cell preparation process. We previously developed a S&XFM-CD for the expansion of umbilical cord-derived MSCs (UCMSCs). Different culture conditions affect the function of MSCs, which may further affect the therapeutic efficiency and mechanisms of action. In this study, we compared the therapeutic effect and mechanism of UCMSCs in S&XFM-CD (UCMSCS&XFM−CD) in experimental colitis with those in SCM (UCMSCSCM). UCMSCS&XFM−CD exhibited better therapeutic effects than UCMSCSCM by body weight, disease activity index, and histological colitis score. UCMSCS&XFM−CD or UCMSCSCM migrated to the inflammation site of injured colon, but exhibited low levels of recruitment and persistence. Systemic depletion of endogenous macrophages impaired the therapeutic effects of UCMSCSCM and UCMSCS&XFM−CD. Furthermore, UCMSCS&XFM−CD more markedly promoted intestinal macrophage polarisation from M1 to M2 phenotype to produce higher levels of IL-10 and lower levels of TNF-α in colon tissue than UCMSCSCM, while a higher level of IL-4 was produced in UCMSCSCM-treated group. UCMSCS&XFM−CD cocultured with RAW264.7 cells in a transwell system promoted the release of TSG-6 and IL-6, whereas UCMSCSCM increased PGE2 levels. Taken together, we demonstrated that UCMSCs in S&XFM-CD exhibited improved therapeutic effects with altered cytokine secretion in an experimental acute colitis model.
Monitoring the collective behavior of enzymatic nanomotors in vitro and in vivo by PET-CT

Enzyme powered nanomotors hold great potential for biomedical applications, as they show improved diffusion and navigation within biological environments using endogenous fuels. Yet, understanding their collective behavior and tracking them in vivo is paramount for their clinical translation. Here, we report on the in vitro and in vivo study of swarms of self-propelled enzyme-nanomotors and the effect of collective behavior on the nanomotors distribution within the bladder. For that purpose, mesoporous silica nanomotors were functionalized with urease enzymes and gold nanoparticles. Two radiolabeling strategies, i.e. absorption of 124I on gold nanoparticles and covalent attachment of an 18F-labeled prosthetic group to urease, were assayed. In vitro experiments using optical microscopy and positron emission tomography (PET) showed enhanced fluid mixing and collective migration of nanomotors in phantoms containing complex paths. Biodistribution studies after intravenous administration in mice confirmed the biocompatibility of the nanomotors at the administered dose, the suitability of PET to quantitatively track nanomotors in vivo, and the convenience of the 18F-labeling strategy. Furthermore, intravesical instillation of nanomotors within the bladder in the presence of urea resulted in a homogenous distribution after the entrance of fresh urine. Control experiments using BSA-coated nanoparticles or nanomotors in water resulted in sustained phase separation inside the bladder, demonstrating that the catalytic decomposition of urea can provide urease-nanomotors with active motion, convection and mixing capabilities in living reservoirs. This active collective dynamics, together with the medical imaging tracking, constitutes a key milestone and a step forward in the field of biomedical nanorobotics, paving the way towards their use in theranostic applications.
Animal identification, recording and evaluation - Interbull's perspectives.

Genetic improvement of dairy cattle starts with the establishment of selection goals and is realized through the recording of genealogical and performance data, the application of genetic evaluation models and finally the actual selection and mating of the parents of the next generation. Reproductive technologies made it possible the use of animals selected within a single population to contribute genes to the genetic makeup of any population in the world, leading to a globalization of the dairy breeds. International trade of dairy genetics needed reliable tools to compare studs from different origins and this originated Interbull as the international network for dairy cattle improvement. Interbull made it possible to compare Artificial Insemination bulls from all over the world, but also became a cooperative effort to improve the national genetic evaluation programs. Only countries having national animal identification and recording programs are able to develop their own genetic evaluation schemes and, consequently, participate and benefit from Interbull services.
COPII Sec23 proteins form isoform-specific ER exit sites with differential effects on polarized growth

COPII, a coat of proteins that form vesicles on the ER, mediates vesicle traffic from the ER to the Golgi. In contrast to metazoans that have few genes encoding each COPII component, plants have expanded these gene families leading to the hypothesis that plant COPII has functionally diversified. Here, we analyzed the gene families encoding for the Sec23/24 heterodimer in the moss Physcomitrium (Physcomitrella) patens. In P. patens, Sec23 and Sec24 gene families are each comprised of seven genes. Silencing the Sec23/24 genes revealed isoform specific contributions to polarized growth, with the closely related Sec23D/E and Sec24C/D essential for protonemal development. Focusing on the Sec23 gene family, we discovered that loss of Sec23D alters ER morphology, increases ER stress, inhibits trafficking to the Golgi and to the plasma membrane in tip growing protonemata. In contrast, the remaining five Sec23 genes are dispensable for tip growth. While Sec23A/B/C/F/G do not quantitatively affect ER to Golgi trafficking in protonemata, they do contribute to secretion to the plasma membrane. Of the three highly expressed Sec23 isoforms in protonemata, Sec23G forms ER exit sites that are larger than Sec23B and Sec23D and do not overlap with Sec23D. Furthermore, ER exit sites labeled by Sec23B or Sec23G form in the absence of Sec23D. These data suggest that Sec23D/E form unique ER exit sites contributing to secretion that is essential for tip growing protonemata.
A proteomic approach to investigate the response of tef (Eragrostis tef) to drought

xii Chapter 1: Introduction . 1 1.1 Tef crop general information. 1 1.2 Tef morphology and plant growth . 2 1.3 Tolerance to biotic and abiotic stresses . 3 1.3. 1 Biotic stresses . 4 1.3. 2 Abiotic stresses . 4 1.3. 2.1 Salt stress . 4 1.3. 2.2 Soil acidity . 4 1.3. 2.3 Drought stress . 5 1.4 Genomics research in tef . 7 1.4. 1 Breeding approaches in tef . 7 1.4. 2 Tef genome and transcriptome sequencing . 9 1.5 Proteomics . 9 1.5. 1 Mass spectrometry-based approaches . 10 1.5. 2 Proteomics to study stress response in crop plants . 11 1.5. 3 Proteomics research in tef . 12 1.6 Objectives of this study . 13 Chapter 2: Tef physiological characterisation . 14 2.
Composition, Structure, and PGPR Traits of the Rhizospheric Bacterial Communities Associated With Wild and Cultivated Echinocactus platyacanthus and Neobuxbaumia polylopha

The Queretaro semi-desert in central Mexico is the most southern extension of the Chihuahua desert. This semi-arid zone shelters a vast cactus diversity with many endemic species. Currently, two cacti species from this semi-desert namely, Echinocactus platyacanthus and Neobuxbaumia polylopha are under a threat to their survival. So far, there are no reports on the bacterial communities associated with these plants. In this study, we assessed the structure and diversity of the rhizospheric bacterial communities associated with Echinocactus platyacanthus and Neobuxbaumia polylopha growing in wild and cultivated conditions. Samples of E. platyacanthus were also approached with culture-based methods in search of isolates with plant growth promoting abilities. Metagenomic DNA was extracted from rhizospheric samples and used for Illumina sequencing of the 16S rRNA gene. α-diversity and amplicon sequence variant (ASV) richness were higher in both groups of E. platyacanthus samples. All samples accounted for 14 phyla, and the major 6 were common to all treatments. The dominant phyla in all four sample groups were Actinobacteria and Proteobacteria. Analysis at family and genus levels showed association patterns with the cultivated samples from both species grouping together, while the wild samples of each cactus species were grouping apart. High abundance values of Rubrobacteraceae (15.9–18.4%) were a characteristic feature of wild E. platyacanthus samples. In total, 2,227 ASVs were scored in all 12 rhizospheric samples where E. platyacanthus samples showed higher richness with 1,536 ASVs. Regarding the growing conditions, both groups of cultivated samples were also richer accounting for 743 and 615 ASVs for E. platyacanthus and N. polylopha, respectively. The isolates from E. platyacanthus rhizosphere were mainly assigned to Bacilli and Gammaproteobacteria. In total 35 strains were assayed for PGPR traits (IAA and siderophore production, phosphate solubilization, and fungal growth inhibition). Strains obtained from plants growing in the wild displayed better PGPR characteristics, stressing that naturally occurring wild plants are a source of bacteria with diverse metabolic activities, which can be very important players in the adaptation of cacti to their natural environments.
A Meta-Analysis of Transcranial Direct Current Stimulation on Substance and Food Craving: What Effect Do Modulators Have?

Substance addiction and food addiction are significant social problems worldwide. In previous studies of substance addiction, transcranial direct current stimulation (tDCS) has been used to influence craving of substance or food. However, the reported effects are not always consistent due to inconsistent experimental settings. The way modulators influence the effect of tDCS on substance addiction is worth exploring. This meta-analysis was conducted to estimate the effect size of tDCS on substance and food craving and to investigate the influence of potential modulators. We systemically identiﬁed and reviewed studies on substance/food craving using tDCS that were published between January 2008 to January 2020. A total of 32 eligible studies were identified. Hedges' g was computed as an indicator of the effect of tDCS and some potential moderators (substance type, stimulation sites, current intensities, number of sessions, duration of stimulation, and study design) were examined using subgroup analysis. Random effects analysis revealed a total medium effect size [Hedges' g = 0.536, 95% confidence interval (CI): 0.389–0.683, after adjusting Hedges' g = 0.416, 95% CI: 0.262–0.570] preferring active over sham stimulation to reduce craving. A significant difference was observed between the number of sessions (repeated stimulation was better than single stimulation). The duration of stimulation may have a positive influence on the effects of tDCS. No other significant differences were found in other subgroups analysis. In conclusion, our results provided evidence that tDCS can be an effective way to reduce craving of substance or food, and longer multiple stimulus durations in all can more effectively reduce craving; however, the influences of modulators still need be to be examined in depth in future.
Expert Opinions and Consensus Recommendations for the Evaluation and Management of Insomnia in Clinical Practice: Joint Statements of Five Italian Scientific Societies

Background Insomnia is the most commonly reported sleep problem in industrialized countries worldwide being present in about 36.8% of the general population. In Italy, such a percentage seems to be even higher. Although insomnia can be an independent disorder, it is most frequently observed as a comorbid condition and may precipitate, exacerbate, or prolong a broad range of comorbid conditions including physical and mental illnesses. Evaluating and targeting insomnia in the Italian clinical practice should be a priority. Methods The present expert options and recommendations development process was based on the RAND/UCLA Appropriateness Method for conceptualizing, designing, and carrying out the appropriateness of procedures for the diagnosis and treatment. Only available options in Italy were taken into considerations. Results We evaluated 12 international guidelines and 12 most recent systematic reviews for insomnia evaluation and treatment produced in the last 10 years. Conclusions Our findings suggested that symptoms of insomnia must always be assessed in the Italian clinical practice by evaluating nocturnal and daytime symptoms, comorbid conditions and lifestyle. In a patient with chronic insomnia with and without comorbidity, insomnia treatment should be always initiated. CBT-Insomnia therapy should be the first option accordingly to availability. The choice of the drug should be based on different factors such as type of insomnia, age, comorbidities, and potential side effects. Melatonin 2 mg prolonged release should be the first choice in subjects >55 years. If the choice would be a Z-drug or a short-acting benzodiazepine (in subjects <65 years old) or a sedating antidepressant, the use should be in the short term (≤4 weeks) and then proceeds to tapering under clinical monitoring
Extraversion, Neuroticism, and Employee Voice: A Conservation of Resources Perspective

Drawing on the Conservation of Resources (COR) theory, we constructed a model about how two of Big-Five personality traits, extraversion and neuroticism, respectively, influence employee voice through an indirect effect of emotional exhaustion. We distributed two wave surveys to 435 employees and their supervisors in a Chinese state-owned bank. Our analyses indicated that extraversion had a positive indirect effect on employee voice via emotional exhaustion, whereas neuroticism had a negative indirect effect on employee voice via emotional exhaustion. We concluded by discussing our theoretical implications with research on employee voice and COR. Additionally, we discussed our practical implications for managerial practices and for the general public.