Miracle-dz/UniFAR-FTUs huggingface dataset:
Video-Assisted Thoracic Surgery Lobectomy

Video-assisted thoracoscopic surgery (VATS) has been established as the surgical approach of choice for lobectomy in patients with early-stage non-small cell lung cancer (NSCLC). Patients with clinical stage I NSCLC with no lymph node metastasis are considered candidates for VATS lobectomy. To rule out the presence of metastasis to lymph nodes or distant organs, patients should undergo meticulous clinical staging. Assessing patients’ functional status is required to ensure that there are no medical contraindications, such as impaired pulmonary function or cardiac comorbidities. Although various combinations of the number, size, and location of ports are available, finding the best method of port placement for each surgeon is fundamental to maximize the efficiency of the surgical procedure. When conducting VATS lobectomy, it is always necessary to comply with the following oncological principles: (1) the vessels and bronchus of the target lobe should be individually divided, (2) systematic lymph node dissection is mandatory, and (3) touching the lymph node itself and rupturing the capsule of the lymph node should be minimized. Most surgeons conduct the procedure in the following sequence: (1) dissection along the hilar structure, (2) fissure division, (3) perivascular and peribronchial dissection, (4) individual division of the vessels and bronchus, (5) specimen retrieval, and (6) mediastinal lymph node dissection. Surgeons should obtain experience in enhancing the exposure of the dissection target and facilitating dissection. This review article provides the basic principles of the surgical techniques and practical maneuvers for performing VATS lobectomy easily, safely, and efficiently.
Optimal distribution-preserving downsampling of large biomedical data sets (opdisDownsampling).

MOTIVATION The size of today's biomedical data sets pushes computer equipment to its limits, even for seemingly standard analysis tasks such as data projection or clustering. Reducing large biomedical data by downsampling is therefore a common early step in data processing, often performed as random uniform class-proportional downsampling. In this report, we hypothesized that this can be optimized to obtain samples that better reflect the entire data set than those obtained using the current standard method. RESULTS By repeating the random sampling and comparing the distribution of the drawn sample with the distribution of the original data, it was possible to establish a method for obtaining subsets of data that better reflect the entire data set than taking only the first randomly selected subsample, as is the current standard. Experiments on artificial and real biomedical data sets showed that the reconstruction of the remaining data from the original data set from the downsampled data improved significantly. This was observed with both principal component analysis and autoencoding neural networks. The fidelity was dependent on both the number of cases drawn from the original and the number of samples drawn. CONCLUSIONS Optimal distribution-preserving class-proportional downsampling yields data subsets that reflect the structure of the entire data better than those obtained with the standard method. By using distributional similarity as the only selection criterion, the proposed method does not in any way affect the results of a later planned analysis.
Theoretical investigation of solid hydrogen and deuterium

Solid hydrogen forms at extreme conditions, under high pressures. Although the hydrogen atom is easy to understand theoretically, when interacting in the solid state it becomes complicated. Up to now, five different solid phases have been confirmed experimentally and theory has predicted numerous competing crystal candidates. The goal is to obtain solid metallic hydrogen which has been predicted theoretically eighty years ago and has since been considered the holy grail of high pressure science. In nature, this form of matter is believed to exist at the core of large planets like Jupiter and Saturn, being responsible for the planets’ large magnetic fields. Understanding the different phases of hydrogen is a test for our most advanced theories of quantum mechanics in condensed matter and it is fundamentally important for both planetary and material science. Recently discovered solid phase IV is stabilized by entropy and therefore only exists at relatively high temperatures. Using molecular dynamics (MD) I studied the room temperature behavior of phase IV starting with the ground state candidate structures reported in the literature. Additionally, I devised a velocity projection method for extracting Raman spectra from MD in light of direct comparison to experiment. My results helped establish the true nature of phase IV and validated the structure against experimental data. Applying the same method to the previously proposed C2/c crystal structure, I obtained results that confirm this structure is the best candidate for phase III. Within the last year, a new phase V of solid hydrogen was discovered in Raman experiments. While attempting to identify the crystal structure associated with this new phase, I discovered a manifestation of solid hydrogen in the form of long polymeric chains that could be stabilized by a charge density wave. Here I discuss the possibility of such a state of matter as an intermediate on the path to molecular dissociation of hydrogen. Chains could, however, be a spurious structure the effect of a subtle non-convergence problem in the MD, which could
The Role of Serial Right Heart Catheterization Survey in Patients Awaiting Heart Transplant on Ventricular Assist Device

Current guidelines recommend serial right heart catheterization (RHC) to survey pulmonary hypertension in patients awaiting heart transplant. However, the role and impact of this surveillance is unclear in patients with a left ventricular assist device (LVAD). We reviewed our surveillance RHC protocol to determine whether useful data were obtained to justify the risks of serial invasive procedures (i.e., excessive bleeding). Between January 2015 and December 2018, 78 patients who received an LVAD as bridge-to-transplant (BTT) were included in this study. Routine RHC surveillance was performed every 6 months. Hemodynamic variables were retrospectively collected and reviewed. In 78 patients, 205 RHCs were analyzed. Median patient age was 54 years (IQR 46–61), and 64 (82%) were male. Thirty-six patients (46%) had pulmonary vascular resistance (PVR) ≤ 3 Wood units (WUs), and 42 patients (54%) had PVR > 3 WUs before LVAD. After LVAD implantation, mean PVR decreased by 36% from 3.8 ± 2.1 to 2.4 ± 1.1 WUs (p < 0.001) at 6 months and stabilized below 3 WUs at all post-LVAD time points. Four patients (11%) with pre-LVAD PVR ≤ 3 and 16 patients (38%) with a pre-LVAD PVR > 3 had PVR > 3 at least once during RHC survey. Of the 56 (76%) transplanted patients, six (40%) of 15 patients with a post-LVAD PVR >3 at least once developed moderate-to-severe right ventricular dysfunction. Although PVR significantly decreased after LVAD implant, PVR values fluctuated, particularly for those with pre-LVAD PVR > 3.0 WUs. Routine RHC appears valid for all BTT patients.
Freeze-dried bovine amniotic membrane as a cell delivery scaffold in a porcine model of radiation-induced chronic wounds

Background Locoregional stem cell delivery is very important for increasing the efficiency of cell therapy. Amnisite BA (Amnisite) is a freeze-dried amniotic membrane harvested from bovine placenta. The objective of this study was to investigate the retention of cells of the stromal vascular fraction (SVF) on Amnisite and to determine the effects of cell-loaded Amnisite in a porcine radiation-induced chronic wound model. Methods Initially, experiments were conducted to find the most suitable hydration and incubation conditions for the attachment of SVF cells extracted from pig fat to Amnisite. Before seeding, SVFs were labeled with PKH67. The SVF cell-loaded Amnisite (group S), Amnisite only (group A), and polyurethane foam (group C) were applied to treat radiation-induced chronic wounds in a porcine model. Biopsy was performed at 10, 14, and 21 days post-operation for histological analysis. Results Retaining the SVF on Amnisite required 30 minutes for hydration and 1 hour for incubation. A PKH67 fluorescence study showed that Amnisite successfully delivered the SVF to the wounds. In histological analysis, group S showed increased re-epithelialization and revascularization with decreased inflammation at 10 days post-operation. Conclusions SVFs had acceptable adherence on hydrated Amnisite, with successful cell delivery to a radiation-induced chronic wound model.
“If I’d Had Something Like SAFE at the Time, Maybe I Would’ve Left Him Sooner.”—Essential Features of eHealth Interventions for Women Exposed to Intimate Partner Violence: A Qualitative Study

Approximately one in three women worldwide experiences intimate partner violence and abuse (IPVA) in her lifetime. Despite its frequent occurrence and severe consequences, women often refrain from seeking help. eHealth has the potential to remove some of the barriers women face in help seeking and disclosing. To guarantee the client-centeredness of an (online) intervention it is important to involve the target group and people with expertise in the development process. Therefore, we conducted an interview study with survivors and professionals, in order to assess needs, obstacles, and wishes with regard to an eHealth intervention for women experiencing IPVA. Semi-structured interviews were conducted with 16 women (8 survivors and 8 professionals) between 22 and 52 years old, with varied experiences of IPVA and help. Qualitative data was analyzed using a grounded theory approach and open thematic coding. During analysis we identified a third stakeholder group within the study population: survivor-professionals, with both personal experiences of and professional knowledge on IPVA. All stakeholder groups largely agree on the priorities for an eHealth intervention: safety, acknowledgment, contact with fellow survivors, and help. Nevertheless, the groups offer different perspectives, with the survivor-professionals functioning as a bridge group between the survivors and professionals. The groups prioritize different topics. For example, survivors and survivor-professionals highlighted the essential need for safety, while professionals underlined the importance of acknowledgment. Survivor-professionals were the only ones to emphasize the importance of addressing various life domains. The experiences of professionals and survivors highlight a broad range of needs and potential obstacles for eHealth interventions. Consideration of these findings could improve the client-centeredness of existing and future (online) interventions for women experiencing IPVA.
Age differences in social-cognitive abilities across the stages of adulthood and path model investigation of adult social cognition

ABSTRACT Accumulating evidence points toward an association between older age and performance decrements in social cognition (SC). We explored age-related variations in four components of SC: emotion recognition, theory of mind, social judgment, and blame attributions. A total of 120 adults divided into three stages (18–34 years, 35–59 years, 60–85 years) completed a battery of SC. Between and within age-group differences in SC were investigated. Path analyses were used to identify relationships among the components. Emotion recognition and theory of mind showed differences beginning either in midlife, or after. Blame attributions and social judgment did not show a significant difference. However, social judgment varied significantly within groups. Path models revealed a relationship between emotion recognition and theory of mind. Findings highlight age-related differences in some components and a link between two components. Strategies promoting social functioning in aging might help to maintain or improve these abilities over time.
Correction of sensor crosstalk error in Exhalyzer D multiple-breath washout device significantly impacts outcomes in children with cystic fibrosis.

RATIONALE Nitrogen multiple-breath washout is an established technique to assess functional residual capacity and ventilation inhomogeneity in the lung. Accurate measurement of gas concentrations is essential for the appropriate calculation of clinical outcomes. OBJECTIVES We investigated the accuracy of oxygen and carbon dioxide gas sensor measurements used for the indirect calculation of nitrogen concentration in a commercial multiple-breath washout device (Exhalyzer D, Eco Medics AG, Duernten, Switzerland) and its impact on functional residual capacity and lung clearance index. METHODS High precision calibration gas mixtures and mass spectrometry were used to evaluate sensor output. We assessed the impact of corrected signal processing on multiple-breath washout outcomes in a dataset of healthy children and children with cystic fibrosis using custom analysis software. RESULTS We found inadequate correction for the cross sensitivity of the oxygen and carbon dioxide sensors in the Exhalyzer D device. This results in an overestimation of expired nitrogen concentration, and consequently multiple-breath washout outcomes. Breath-by-breath correction of this error reduced the mean (SD) cumulative expired volume by 19.6 (5.0)%, functional residual capacity by 8.9 (2.2)%, and lung clearance index by 11.9 (4.0)%. It also substantially reduced the level of the tissue nitrogen signal at the end of measurements. CONCLUSIONS Inadequate correction for cross sensitivity in the oxygen and carbon dioxide gas sensors of the Exhalyzer D device leads to an overestimation of functional residual capacity and lung clearance index. Correction of this error is possible and could be applied by re-analyzing the measurements in an updated software version.
Cucumber RDR1s and cucumber mosaic virus suppressor protein 2b association directs host defence in cucumber plants

Abstract RNA‐dependent RNA polymerases (RDRs) regulate important aspects of plant development and resistance to pathogens. The role of RDRs in virus resistance has been demonstrated using siRNA signal amplification and through the methylation of viral genomes. Cucumber (Cucumis sativus) has four RDR1 genes that are differentially induced during virus infection: CsRDR1a, CsRDR1b, and duplicated CsRDR1c1/c2. The mode of action of CsRDR1s during viral infection is unknown. Transient expression of the cucumber mosaic virus (CMV)‐2b protein (the viral suppressor of RNA silencing) in cucumber protoplasts induced the expression of CsRDR1c, but not of CsRDR1a/1b. Results from the yeast two‐hybrid system showed that CsRDR1 proteins interacted with CMV‐2b and this was confirmed by bimolecular fluorescence complementation assays. In protoplasts, CsRDR1s localized in the cytoplasm as punctate spots. Colocalization experiments revealed that CsRDR1s and CMV‐2b were uniformly dispersed throughout the cytoplasm, suggesting that CsRDR1s are redistributed as a result of interactions. Transient overexpression of individual CsRDR1a/1b genes in protoplasts reduced CMV accumulation, indicating their antiviral role. However, overexpression of CsRDR1c in protoplasts resulted in relatively higher accumulation of CMV and CMVΔ2b. In single cells, CsRDR1c enhances viral replication, leading to CMV accumulation and blocking secondary siRNA amplification of CsRDR1c by CMV‐2b protein. This suggests that CMV‐2b acts as both a transcription factor that induces CsRDR1c (controlling virus accumulation) and a suppressor of CsRDR1c activity.
The Natural History of Rectal Gonococcal and Chlamydial Infections: the ExGen Study.

BACKGROUND The duration of rectal gonococcal and chlamydial infection remains unknown. This basic epidemiologic parameter is needed to understand transmission dynamics. METHODS We conducted a prospective, longitudinal, observational, cohort study of 140 men who have sex with men (MSM) at-risk of gonorrhea and chlamydia acquisition. For 48 weeks, enrolled men collected rectal swabs (Aptima multitest kit) at home and responded to an electronic survey about sexual behavior and health conditions weekly. Swabs remained untested until participants completed the study. We used Kaplan Meier estimates to determine the median duration of infection, censoring infections for treatment, loss-to-follow-up and end-of-study. We used Log-rank test to compare duration of infection by HIV status, history of infection with gonorrhea or chlamydia, and co-infection with the other pathogen. RESULTS 140 enrolled MSM contributed 70.5 person years of follow-up. Eighteen men had 20 incident rectal gonococcal infections, which persisted for 2 - 23 weeks; 30% were censored for treatment. The estimated median duration of rectal gonorrhea was 9 weeks (95% CI: 3-12 weeks). Twenty-four men experienced 32 rectal chlamydial infections, persisting between 2 to 42 weeks; 60% were censored. The estimated duration of rectal chlamydia was 13 weeks (95% CI: 6 weeks - undefined). There were no differences in the duration of rectal gonorrhea or chlamydia by HIV status, history of chlamydia/gonorrhea or co-infection. CONCLUSIONS On average, rectal gonorrhea and chlamydial infections last 2-3 months, though some infections some persist for 6-11 months. Further understanding into predictors of persistence are needed.
Evolution and Physiology of Amphibious Yeasts.

Since the emergence of the first fungi some 700 million years ago, unicellular yeast-like forms have emerged multiple times in independent lineages via convergent evolution. While tens to hundreds of millions of years separate the independent evolution of these unicellular organisms, they share remarkable phenotypic and metabolic similarities, and all have streamlined genomes. Yeasts occur in every aquatic environment yet examined. Many species are aquatic; perhaps most are amphibious. How these species have evolved to thrive in aquatic habitats is fundamental to understanding functions and evolutionary mechanisms in this unique group of fungi. Here we review the state of knowledge of the physiological and ecological diversity of amphibious yeasts and their key evolutionary adaptations enabling survival in aquatic habitats. We emphasize some genera previously thought to be exclusively terrestrial. Finally, we discuss the ability of many yeasts to survive in extreme habitats and how this might lend insight into ecological plasticity, including amphibious lifestyles. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews. org/page/journal/pubdates for revised estimates.
Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture

Nitrate commands genome‐wide gene expression changes that impact metabolism, physiology, plant growth, and development. In an effort to identify new components involved in nitrate responses in plants, we analyze the Arabidopsis thaliana root phosphoproteome in response to nitrate treatments via liquid chromatography coupled to tandem mass spectrometry. 176 phosphoproteins show significant changes at 5 or 20 min after nitrate treatments. Proteins identified by 5 min include signaling components such as kinases or transcription factors. In contrast, by 20 min, proteins identified were associated with transporter activity or hormone metabolism functions, among others. The phosphorylation profile of NITRATE TRANSPORTER 1.1 (NRT1.1) mutant plants was significantly altered as compared to wild‐type plants, confirming its key role in nitrate signaling pathways that involves phosphorylation changes. Integrative bioinformatics analysis highlights auxin transport as an important mechanism modulated by nitrate signaling at the post‐translational level. We validated a new phosphorylation site in PIN2 and provide evidence that it functions in primary and lateral root growth responses to nitrate.
Fis1 ablation in the male germline disrupts mitochondrial morphology and mitophagy, and arrests spermatid maturation

ABSTRACT Male germline development involves choreographed changes to mitochondrial number, morphology and organization. Mitochondrial reorganization during spermatogenesis was recently shown to require mitochondrial fusion and fission. Mitophagy, the autophagic degradation of mitochondria, is another mechanism for controlling mitochondrial number and physiology, but its role during spermatogenesis is largely unknown. During post-meiotic spermatid development, restructuring of the mitochondrial network results in packing of mitochondria into a tight array in the sperm midpiece to fuel motility. Here, we show that disruption of mouse Fis1 in the male germline results in early spermatid arrest that is associated with increased mitochondrial content. Mutant spermatids coalesce into multinucleated giant cells that accumulate mitochondria of aberrant ultrastructure and numerous mitophagic and autophagic intermediates, suggesting a defect in mitophagy. We conclude that Fis1 regulates mitochondrial morphology and turnover to promote spermatid maturation.
Ammonia removal from poultry manure leachate via struvite precipitation: a strategy for more efficient anaerobic digestion

To improve poultry waste management, the feasibility of enabling efficient anaerobic digestion of poultry manure through reduction of ammonia accumulation is examined. This study employs struvite precipitation to control ammonia accumulation, and focuses on the efficacy of ammonia removal under neutral reaction conditions (pH = 7). The impacts of phosphate and magnesium additives, pH, temperature and the N:Mg:P molar ratio are quantified. Magnesium chloride (MgCl2 • 6H2O) and monopotassium phosphate (KH2PO4) are shown to be the most efficient combination of additives for total ammoniacal nitrogen (TAN) reduction of poultry manure leachate under neutral reaction conditions (pH = 7), demonstrating a TAN reduction of 90.3%. Modification of molar ratios (NH4:Mg:PO4) evidenced no significant benefit with regard to TAN reduction. However, increasing the fraction of supplementary magnesium resulted in a statistically significant (p < 0.05) decrease in phosphate concentration within the leachate. This study demonstrates the advantages of struvite precipitation, as a method of ammonia control, to improve anaerobic digestion and hence management of poultry manure. Although an effective means of TAN control, struvite precipitation from poultry manure is an ineffective means of obtaining pure struvite due to the formation of co-precipitates.
The Visual Opsin Gene Repertoires of Teleost Fishes: Evolution, Ecology, and Function.

Visual opsin genes expressed in the rod and cone photoreceptor cells of the retina are core components of the visual sensory system of vertebrates. Here, we provide an overview of the dynamic evolution of visual opsin genes in the most species-rich group of vertebrates, teleost fishes. The examination of the rich genomic resources now available for this group reveals that fish genomes contain more copies of visual opsin genes than are present in the genomes of amphibians, reptiles, birds, and mammals. The expansion of opsin genes in fishes is due primarily to a combination of ancestral and lineage-specific gene duplications. Following their duplication, the visual opsin genes of fishes repeatedly diversified at the same key spectral-tuning sites, generating arrays of visual pigments sensitive from the ultraviolet to the red spectrum of the light. Species-specific opsin gene repertoires correlate strongly with underwater light habitats, ecology, and color-based sexual selection. Expected final online publication date for the Annual Review of Cell and Developmental Biology, Volume 37 is October 2021. Please see http://www.annualreviews. org/page/journal/pubdates for revised estimates.