Miracle-dz/UniFAR-FTUs huggingface dataset:
Perioperative complications of laparoscopic inguinal hernia repair in India: a prospective observational study

Purpose These days laparoscopic inguinal hernia surgery, both totally extraperitoneal (TEP) and transabdominal preperitoneal (TAPP), is a commonly performed procedure due to advancements in laparoscopic instruments and the availability of skilled laparoscopic surgeons. The purpose of this study was to compare the perioperative complications of these two procedures. Methods This was a prospective observational study between July 2019 and December 2020. Perioperative complications were compared with a 6-month follow-up. It included 144 patients, of whom 71 underwent TAPP repair and 73 underwent TEP repair. The selection was based on the surgeon’s choice. Results Early postoperative complications were scrotal edema (12 cases in TEP and 16 in TAPP), urinary retention (one case in TEP), ecchymosis (six cases in TEP and two in TAPP), and scrotal subcutaneous emphysema (two cases in TEP). On follow-up, seroma was found in a total of 22 cases, of which 12 were TEP and 10 were TAPP. While only one case of TAPP developed surgical site infection. There was no statistically significant difference in hospital stay between the two groups (p = 0.58). The pain scores significantly decreased throughout recovery and were comparable between the groups. Neither group experienced a recurrence during the 6-month follow-up. Fifty-eight patients developed Clavien-Dindo grade I complications, one had grade II, and three had grade IIIa complications. Conclusion With the increasing experience of the surgical fraternity in laparoscopic surgery, TEP and TAPP were proven to be comparable in terms of duration of surgery, postoperative complications, hospital stay, pain scores, and recurrence during the 6-month follow-up.
An atypical airway cast

Abstract A 60-year-old man intubated for airway protection after smoke inhalation was found to have decompensated hypercapnic respiratory failure. Fiberoptic bronchoscopy revealed obstructive airway slough and pseudomembrane, a manifestation of severe inhalation injury. Veno-venous extracorporeal membrane oxygenation was established for stabilization. The airway casts were removed successfully with periprocedural veno-venous extracorporeal membrane oxygenation support.
The Bone Marrow Microenvironment in Immune-Mediated Inflammatory Diseases: Implications for Mesenchymal Stromal Cell-Based Therapies

Abstract Bone marrow (BM)-derived mesenchymal stromal cells (MSCs) are promising candidates for cell-based therapy for several immune-mediated inflammatory diseases (IMIDs) due to their multiplicity of immunomodulatory and reparative properties and favorable safety profile. However, although preclinical data were encouraging, the clinical benefit demonstrated in clinical trials of autologous MSC transplantation in a number of conditions has been less robust. This may be explained by the growing body of evidence pointing to abnormalities of the bone marrow microenvironment in IMIDs, including impaired MSC function. However, it is not currently known whether these abnormalities arise as a cause or consequence of disease, the role they play in disease initiation and/or progression, or whether they themselves are targets for disease modification. Here, we review current knowledge about the function of the BM microenvironment in IMIDs including multiple sclerosis, systemic lupus erythematosus, rheumatoid arthritis, and type I diabetes, focusing on MSCs in particular. We predict that an improved understanding of disease-related changes in the bone marrow microenvironment including the role of MSCs in vivo, will yield new insights into pathophysiology and aid identification of new drug targets and optimization of cell-based therapy in IMIDs.
Coastal sand dune vegetation: an extreme case of species invasion

The coastal sand-dune flora of the Gulf and Carib bean region of Mexico was analyzed to understand differ ences in floristic composition and richness found along the coast. Each of the 655 species reported was classified accord ing to its ecology and distribution range by checking herbaria specimens, literature and specialists. Three groups were formed: (a) species with predominantly coastal distribution; (b) ruderal or secondary species frequently found inland, common of disturbed areas such as roadsides, abandoned fields or forming part of secondary growths; (c) inland spe cies frequently found in other vegetation types such as tropi cal dry or seasonal forest and grassland. A total of 71 coastal species, 237 ruderal/secondary and 336 species from other community types were found. The distribution of these groups was analyzed along 44 sites of the Gulf and Caribbean, in the different dune habitats and for the dominant growth forms. Coastal species are more widely distributed; they predomi nate in habitats with sand movement and the herbaceous component prevails. Ruderal/secondary species and especially those belonging to other vegetation types frequently appear in only one or two sites occupying more protected or stabilized habitats. The two latter groups considerably increase species richness of sand dune flora, but also pose interesting prob lems for dune conservation.
Acceptance and Commitment Therapy is feasible for people with acquired brain injury: A process evaluation of the BrainACT treatment

Objective To evaluate the feasibility of Acceptance and Commitment Therapy for people with acquired brain injury. Design A process evaluation of the BrainACT treatment was conducted alongside a randomised controlled trial. Setting Psychology departments of hospitals and rehabilitation centres. Subjects Tweny-seven participants with acquired brain injury and 11 therapists. Intervention BrainACT is an Acceptance and Commitment Therapy adapted for the needs and possible cognitive deficits of people with acquired brain injury, provided in eight one-hour face-to-face or video-conference sessions. Measurements The attendance and compliance rates, engagement, satisfaction, and perceived barriers and facilitators for delivery in clinical practice were investigated using semi-structured interviews with participants and therapists and therapy logs. Results 212 of the 216 sessions in total were attended and 534 of the 715 protocol elements across participants and sessions were delivered. Participants were motivated and engaged. Participants and therapists were satisfied with the intervention and participants reported to have implemented skills in their daily routines acquired during therapy. Key strengths are the structure provided with the bus of life metaphor, the experiential nature of the intervention, and the materials and homework. Participants and therapists often preferred face-to-face sessions, however, when needed video-conferencing is a good alternative. Conclusion BrainACT is a feasible intervention for people with anxiety and depressive symptoms following acquired brain injury. However, when the content of the intervention is too extensive, we recommend adding two extra sessions.
Epithelial Immune Cell Response to Initial Soft Contact Lens Wear in the Human Corneal and Conjunctival Epithelium

Purpose The purpose of this study was to assess the immediate ocular immune response to soft contact lens (CL) wear by examining presumed epithelial immune cell (EIC) density and morphology at the central, peripheral, limbal cornea, and conjunctiva. Methods Fifty-four participants naïve to CL wear (mean age = 24.8 ± 9.8 years, 44% female participants), were examined using in vivo confocal microscopy at baseline and after 2 hours of CL wear (1-Day ACUVUE MOIST). Images were captured at the central, temporal far peripheral and limbal cornea, and bulbar conjunctiva. EIC density was counted manually and morphology was graded. Differences in EIC parameters pre- and post-CL wear were examined using a generalized estimating equation model with appropriate post hoc analyses. Results After 2 hours of soft CL wear, there was a significant increase in EIC density in all regions other than the central cornea (all P < 0.001). Cell body size was significantly larger, and a higher proportion of participants exhibited EIC with long dendrites after lens wear at the central and peripheral cornea (both P < 0.001). There was a significant increase in the number of participants displaying EIC with thick dendrites at the peripheral (P = 0.04) and limbal cornea (P < 0.001) after lens wear. Conclusions EICs were primarily recruited to the peripheral regions, whereas the central cornea shows no significant recruitment after short-term CL wear. Both central and peripheral corneas exhibited an enhanced antigen capture capacity, whereas migratory capacity was increased in the peripheral corneal regions suggesting EIC activation following a short period of CL wear.
Late Neogene Paleoceanography and Paleoclimatology of the Northeast Indian Ocean (Site 758)

The evolution of oceanic and climatic conditions the northeast Indian Ocean during the last 7 m.y. is revealed in the sediments from Site 758. We present detailed and continuous records of δ 1 8 θ and δ 1 C from planktonic foraminifers, weight percent calcium carbonate, weight percent coarse fraction, magnetic susceptibility, and geomagnetic reversals. Sample spacing of the records ranges from 3 to 10 cm and is equivalent to an average time interval of 2000 to 6000 yr. Despite the fact that core recovery ranged between 100% and 105%, recovery gaps as large as 2.7 m occurred at nearly every break between advanced hydraulic piston cores. Approximately 12% of the late Neogene sequence was not recovered in each of the two holes drilled at Site 758. To circumvent the discontinuity introduced by the gaps, a composite depth section was constructed from multiple cores taken from offset holes at Site 758. The resulting composite depth section extends continuously from 0 to 116 mbsf, from the Holocene to the upper Miocene. A detailed chronostratigraphy is based on geomagnetic reversals which extend from the Brunhes Chron to Chron 6, and on δ O stages 1 through 105, which span from 0 to 2.5 Ma. The δ 1 8 θ record is dominated by a ~40-k.y. cycle in the late Pliocene and early Pleistocene, and is followed by a change to a ~lOO-k.y. cycle in the late Pleistocene. The mid-Pleistocene transition between these two modes of variability occurs between δ 1 8 θ stages 25 and 22 (between 860 and 800 Ka). Thirteen major volcanic ash horizons from the Indonesian arc are observed throughout the sedimentary section and are dated by their relative position within the geomagnetic reversals and the δ 1 8 θ chronostratigraphy. Since 5 Ma, there has been a long-term decline in weight percent CaCθ3 and CaCθ3 mass accumulation rates, and an associated rise in non-CaCθ3 mass accumulation rates. We attribute these changes to a decrease in CaCθ3 productivity and an increase in terrigenous sedimentation through enhanced riverine input. Such input may be linked to rapid tectonic uplift of the Himalayas and the Tibetan Plateau via mechanisms such as the intensification of the monsoonal rains, increased fluvial erosion, and regional glaciation. The long-term increase in percent coarse fraction since 5 Ma suggests a gradual increase in CaCθ3 preservation. Higher frequency fluctuations in CaCθ3 preservation are superimposed on the long-term trend and are related to climate fluctuations. The abrupt drop (-50%) in CaC03 accumulation at 3.4 Ma signals a dramatic decrease in CaCθ3 production that occurred over much of the Indian Ocean.
Cross-Domain Identification of Multisite Major Depressive Disorder Using End-to-End Brain Dynamic Attention Network

Establishing objective and quantitative imaging markers at individual level can assist in accurate diagnosis of Major Depressive Disorder (MDD). However, the clinical heterogeneity of MDD and the shift to multisite data decreased identification accuracy. To address these issues, the Brain Dynamic Attention Network (BDANet) is innovatively proposed, and analyzed bimodal scans from 2055 participants of the Rest-meta-MDD consortium. The end-to-end BDANet contains two crucial components. The Dynamic BrainGraph Generator dynamically focuses and represents topological relationships between Regions of Interest, overcoming limitations of static methods. The Ensemble Classifier is constructed to obfuscate domain sources to achieve inter-domain alignment. Finally, BDANet dynamically generates sample-specific brain graphs by downstream recognition tasks. The proposed BDANet achieved an accuracy of 81.6%. The regions with high attribution for classification were mainly located in the insula, cingulate cortex and auditory cortex. The level of brain connectivity in p24 region was negatively correlated (<inline-formula> <tex-math notation="LaTeX">$\text{p} < 0.05$ </tex-math></inline-formula>) with the severity of MDD. Additionally, sex differences in connectivity strength were observed in specific brain regions and functional subnetworks (<inline-formula> <tex-math notation="LaTeX">$\text{p} < 0.05$ </tex-math></inline-formula> or <inline-formula> <tex-math notation="LaTeX">$\text{p} < 0.01$ </tex-math></inline-formula>). These findings based on a large multisite dataset support the conclusion that BDANet can better solve the problem of the clinical heterogeneity of MDD and the shift of multisite data. It also illustrates the potential utility of BDANet for personalized accurate identification, treatment and intervention of MDD.
“Returning to the core tasks”: a qualitative interview study about how general practitioners in home health care solved problems during the COVID-19 pandemic

Abstract Objective Optimizing care at home, or home health care (HHC), is necessary as the population of care-dependent older people receiving care at home steadily increases. The COVID-19 pandemic tested Swedish primary care professionals as they provided HHC for a population of very frail older homebound people, but a better understanding of what healthcare workers did to manage the crisis may be useful for the further development of HHC. In this study, we aimed to understand how HHC physicians solved the problems of providing home healthcare during the pandemic to learn lessons on how to improve future HHC. Methods This is a qualitative study of individual interviews with 11 primary care physicians working in HHC (8 women) from 7 primary care practices in Region Stockholm, Sweden. Interviews were conducted between 1 December 2020, and 11 March 2021. The data were analyzed using inductive thematic analysis. Results We generated an overarching theme in our analysis: Physicians focus on core tasks and professional values in response to crisis. This theme incorporated three underlying subthemes describing this response: physicians prioritize and resolve ethically challenging situations in new ways, cultivate the patient perspective, and build on existing teams. Conclusion This study indicates that a healthcare system that gives HHC physicians agency to focus on core tasks and professional values could promote person-centered care.
Yeast as a model eukaryote in drug safety studies

Non-steroidal anti-inflammatory drugs (NSAIDs) are widely used in the treatment of pain and inflammation. However, this group of drugs is associated with serious adverse drug reactions. Previously, we studied the mechanisms underlying toxicity of the NSAID diclofenac using Saccharomyces cerevisiae as model system. We identified the involvement of several mitochondrial proteins, a transporter and cytochrome P450 activity in diclofenac toxicity. In this study, we investigated if these processes are also involved in the toxicity of other NSAIDs. We divided the NSAIDs into three classes based on their toxicity mechanisms. Class I consists of diclofenac, indomethacin and ketoprofen. Mitochondrial respiration and reactive oxygen species play a major role in the toxicity of this class. Metabolism by cytochrome P450s further increases their toxicity, while ABC-transporters decrease the toxicity. Mitochondria and oxidative metabolism also contribute to toxicity of class II drugs ibuprofen and naproxen, but another cellular target dominates their toxicity. Interestingly, ibuprofen was the only NSAID that was unable to induce upregulation of the multidrug resistance response. The class III NSAIDs sulindac, ketorolac and zomepirac were relatively non-toxic in yeast. In conclusion, we demonstrate the use of yeast to investigate the mechanisms underlying the toxicity of structurally related drugs.
Gene set correlation enrichment analysis for interpreting and annotating gene expression profiles

Abstract Pathway analysis, including nontopology-based (non-TB) and topology-based (TB) methods, is widely used to interpret the biological phenomena underlying differences in expression data between two phenotypes. By considering dependencies and interactions between genes, TB methods usually perform better than non-TB methods in identifying pathways that include closely relevant or directly causative genes for a given phenotype. However, most TB methods may be limited by incomplete pathway data used as the reference network or by difficulties in selecting appropriate reference networks for different research topics. Here, we propose a gene set correlation enrichment analysis method, Gscore, based on an expression dataset-derived coexpression network to examine whether a differentially expressed gene (DEG) list (or each of its DEGs) is associated with a known gene set. Gscore is better able to identify target pathways in 89 human disease expression datasets than eight other state-of-the-art methods and offers insight into how disease-wide and pathway-wide associations reflect clinical outcomes. When applied to RNA-seq data from COVID-19-related cells and patient samples, Gscore provided a means for studying how DEGs are implicated in COVID-19-related pathways. In summary, Gscore offers a powerful analytical approach for annotating individual DEGs, DEG lists, and genome-wide expression profiles based on existing biological knowledge.
A reservoir of timescales emerges in recurrent circuits with heterogeneous neural assemblies

The temporal activity of many physical and biological systems, from complex networks to neural circuits, exhibits fluctuations simultaneously varying over a large range of timescales. Long-tailed distributions of intrinsic timescales have been observed across neurons simultaneously recorded within the same cortical circuit. The mechanisms leading to this striking temporal heterogeneity are yet unknown. Here, we show that neural circuits, endowed with heterogeneous neural assemblies of different sizes, naturally generate multiple timescales of activity spanning several orders of magnitude. We develop an analytical theory using rate networks, supported by simulations of spiking networks with cell-type specific connectivity, to explain how neural timescales depend on assembly size and show that our model can naturally explain the long-tailed timescale distribution observed in the awake primate cortex. When driving recurrent networks of heterogeneous neural assemblies by a time-dependent broadband input, we found that large and small assemblies preferentially entrain slow and fast spectral components of the input, respectively. Our results suggest that heterogeneous assemblies can provide a biologically plausible mechanism for neural circuits to demix complex temporal input signals by transforming temporal into spatial neural codes via frequency-selective neural assemblies.
Effect Predictor of Driver Synonymous Mutations Based on Multi-Feature Fusion and Iterative Feature Representation Learning

Accurate identification of driver mutations is crucial in genetic studies of human cancers. While numerous cancer driver missense mutations have been identified, research into potential cancer drivers for synonymous mutations has shown limited success to date. Here, we developed a novel machine learning framework, epSMic, for predicting cancer driver synonymous mutations. epSMic employs an iterative feature representation scheme that facilitates the learning of discriminative features from various sequential models in a supervised iterative mode. We constructed the benchmark datasets and encoded the embedding sequence, physicochemical property, and basic information such as conservation and splicing feature. The evaluation results on benchmark test datasets demonstrate that epSMic outperforms existing methods, making it a valuable tool for researchers in identifying functional synonymous mutations in cancer. We hope epSMic can enable researchers to concentrate on synonymous mutations that have a functional impact on cancer.
Scapular dyskinesia: evolution towards a systems-based approach

Historically, scapular dyskinesia has been used to describe an isolated clinical entity whereby an abnormality in positioning, movement or function of the scapula is present. Based upon this, treatment approaches have focused on addressing local isolated muscle activity. Recently, however, there has been a progressive move towards viewing the scapula as being part of a wider system of movement that is regulated and controlled by multiple factors, including the wider kinetic chain and individual patient-centred requirements. We therefore propose a paradigm shift whereby scapular dyskinesia is seen not in isolation but is considered within the broader context of patient-centred care and an entire neuromuscular system.
Formation and characterization of Group IV semiconductor nanowires

To enable the application to next-generation devices of semiconductor nanowires (NWs), it is important to control their formation and tune their functionality by doping and the use of heterojunctions. In this paper, we introduce formation and the characterization methods of nanowires, focusing on our research results. We describe a top-down method of controlling the size and alignment of nanowires that shows advantages over bottom-up growth methods. The latter technique causes damage to the nanowire surfaces, requiring defect removal after the NW formation process. We show various methods of evaluating the bonding state and electrical activity of impurities in NWs. If an impurity is doped in a NW, mobility decreases due to the scattering that it causes. As a strategy for solving this problem, we describe research into core–shell nanowires, in which Si and Ge heterojunctions are formed in the diameter direction inside the NW. This structure can separate the impurity-doped region from the carrier transport region, promising as a channel for the new ultimate high-mobility transistor.
Impact of folic acid supplementation on the epigenetic profile in healthy unfortified individuals – a randomized intervention trial

ABSTRACT Folate is an essential mediator in one-carbon metabolism, which provides methyl groups for DNA synthesis and methylation. The availability of active methyl groups can be influenced by the uptake of folic acid. We conducted a randomized intervention trial to test the influence of folic acid supplementation on DNA methylation in an unfortified population in Germany. A total of 16 healthy male volunteers (age range 23–61 y) were randomized to receive either 400 μg (n = 9) or 800 μg (n = 7) folic acid supplements daily for 8 weeks. Infinium Human Methylation 450K BeadChip Microarrays were used to assay site-specific DNA methylation across the genome. Microarray analyses were conducted on PBL DNA. We estimated several epigenetic clocks and mean DNA methylation across all autosomal probes on the array. AgeAccel was estimated as the residual variation in each metric. In virtually all participants, both serum and red blood cell (RBC) folate increased successively throughout the trial period. Participants with a larger increase in RBC folate had a larger increase in DNAmAge AgeAccel (Spearman Rho: 0.56, p-value = 0.03). No notable changes in the methylome resulting from the folic acid supplementation emerged. In this population with adequate folate levels derived from diet, an increase in RBC folate had a modest impact on the epigenetic clock predicting chronologic age.