Miracle-dz/UniFAR-FTUs huggingface dataset:
Developing an Interface and Investigating Optimal Parameters for Real-Time Intracardiac Subharmonic-Aided Pressure Estimation

Thisstudy focuses on evaluating the real-time functionality of a customized interface and investigating the optimal parameters for intracardiac subharmonic-aided pressure estimation (SHAPE) utilizing Definity (Lantheus Medical Imaging Inc., North Billerica, MA, USA) and Sonazoid (GE Healthcare, Oslo, Norway) microbubbles. Pressure measurements within the chambers of the heart yield critical information for managing cardiovascular diseases. An alternative to current, invasive, clinical cardiac catheterization procedures is utilizing ultrasound contrast agents and SHAPE to noninvasively estimate intracardiac pressures. Therefore, this work developed a customized interface (on a SonixTablet, BK Ultrasound, Peabody, MA, USA) for real-time intracardiac SHAPE. <italic>In vitro</italic>, a Doppler flow phantom was utilized to mimic the dynamic pressure changes within the heart. Definity (15.0–<inline-formula> <tex-math notation="LaTeX">$22.5~\mu \text{L}$ </tex-math></inline-formula> microspheres corresponding to 0.1–0.15 mL) and Sonazoid (GE Healthcare; 0.4–<inline-formula> <tex-math notation="LaTeX">$1.2~\mu \text{L}$ </tex-math></inline-formula> microspheres corresponding to 0.05–0.15 mL) microbubbles were used. Data were acquired for varying transmit frequencies (2.5–4.0 MHz), and pulse shaping options (square wave and chirp down) to determine optimal transmit parameters. Simultaneously obtained radio frequency data and ambient pressure data were compared. For Definity, the chirp down pulse at 3.0 MHz yielded the highest correlation (<inline-formula> <tex-math notation="LaTeX">$r = - 0.77\,\,\pm \,\,0.2$ </tex-math></inline-formula>) between SHAPE and pressure catheter data. For Sonazoid, the square wave pulse at 2.5 MHz yielded the highest correlation (<inline-formula> <tex-math notation="LaTeX">${r} = - 0.72\,\,\pm \,\,0.2$ </tex-math></inline-formula>). In conclusion, the real-time functionality of the customized interface has been verified, and the optimal parameters for utilizing Definity and Sonazoid for intracardiac SHAPE have been determined.
Interaction between Schwann cells and other cells during repair of peripheral nerve injury

Peripheral nerve injury (PNI) is common and, unlike damage to the central nervous system injured nerves can effectively regenerate depending on the location and severity of injury. Peripheral myelinating glia, Schwann cells (SCs), interact with various cells in and around the injury site and are important for debris elimination, repair, and nerve regeneration. Following PNI, Wallerian degeneration of the distal stump is rapidly initiated by degeneration of damaged axons followed by morphologic changes in SCs and the recruitment of circulating macrophages. Interaction with fibroblasts from the injured nerve microenvironment also plays a role in nerve repair. The replication and migration of injury-induced dedifferentiated SCs are also important in repairing the nerve. In particular, SC migration stimulates axonal regeneration and subsequent myelination of regenerated nerve fibers. This mobility increases SC interactions with other cells in the nerve and the exogenous environment, which influence SC behavior post-injury. Following PNI, SCs directly and indirectly interact with other SCs, fibroblasts, and macrophages. In addition, the inter- and intracellular mechanisms that underlie morphological and functional changes in SCs following PNI still require further research to explain known phenomena and less understood cell-specific roles in the repair of the injured peripheral nerve. This review provides a basic assessment of SC function post-PNI, as well as a more comprehensive evaluation of the literature concerning the SC interactions with macrophages and fibroblasts that can influence SC behavior and, ultimately, repair of the injured nerve.
Influence of Shorea robusta leaf extract treatment on Terminalia arjuna plants over tasar silkworm growth and economic traits

Continuous rearing of tasar silkworm on same Arjun plantations has led to decrease in silkworm commercial characters owing to depleting leaf nutrient quality. Plantations rarely receive manures due to poor economic status of tribal farmers. Considering the presence of vital nutrients and high antinutritional factors in Shorea robusta (Sal), nine treatments of Sal leaf extract having different dilutions and treatment duration were applied over Arjun plants. Tasar silkworm reared on treated Arjun plants revealed significant improvement for larval body weight, cocoon weight, pupa weight, fecundity and reeling parameters. Among treatmentsT4 (500 ml extract + 500 ml water, 3 days interval) has significantly enhanced fecundity by 13% over control, besides enhancing larval weight, pupal weight, filament length and silk weight. On contrary, silkworm reared directly on Sal plants shown high larval mortality (95%) and survived larvae spinned cocoons of inferior quality, this was attributed to high level of anti-nutritional factors in Sal. Thus, supplementation of silkworm nutrition through Sal leaf extract is an eco-friendly, feasible and zero cost approach for tasar farmers.
Comparison of peritoneal function within the first 1 year of peritoneal dialysis between diabetic and non‐diabetic patients

The aim of this study was to compare the changes in peritoneal function and residual renal function in the first year between diabetic and non‐diabetic patients receiving peritoneal dialysis (PD). We extracted 73 incident PD patients (male, 73%; age, 59 ± 15 years) from a previous cohort, and investigated the changes in PD‐related parameters, including the dialysate to plasma ratio of creatinine (D/P Cr) and Kt/V. D/P Cr increased in non‐diabetics, whereas it did not change significantly in diabetic patients. These differences were more pronounced among icodextrin users. On multivariate analysis, the presence of diabetes was independently associated with the changes in D/P Cr. On the contrary, there was no significant difference in the changes of renal Kt/V between the two groups. A higher peritoneal solute transport rate at the start of PD in diabetics was attenuated within 1 year. Icodextrin is thought to have an important role through improving body fluid status.
Staphylococcal Biofilm Development: Structure, Regulation, and Treatment Strategies

In many natural and clinical settings, bacteria are associated with some type of biotic or abiotic surface that enables them to form biofilms, a multicellular lifestyle with bacteria embedded in an extracellular matrix. Staphylococcus aureus and Staphylococcus epidermidis, the most frequent causes of biofilm-associated infections on indwelling medical devices, can switch between an existence as single free-floating cells and multicellular biofilms. During biofilm formation, cells first attach to a surface and then multiply to form microcolonies. SUMMARY In many natural and clinical settings, bacteria are associated with some type of biotic or abiotic surface that enables them to form biofilms, a multicellular lifestyle with bacteria embedded in an extracellular matrix. Staphylococcus aureus and Staphylococcus epidermidis, the most frequent causes of biofilm-associated infections on indwelling medical devices, can switch between an existence as single free-floating cells and multicellular biofilms. During biofilm formation, cells first attach to a surface and then multiply to form microcolonies. They subsequently produce the extracellular matrix, a hallmark of biofilm formation, which consists of polysaccharides, proteins, and extracellular DNA. After biofilm maturation into three-dimensional structures, the biofilm community undergoes a disassembly process that leads to the dissemination of staphylococcal cells. As biofilms are dynamic and complex biological systems, staphylococci have evolved a vast network of regulatory mechanisms to modify and fine-tune biofilm development upon changes in environmental conditions. Thus, biofilm formation is used as a strategy for survival and persistence in the human host and can serve as a reservoir for spreading to new infection sites. Moreover, staphylococcal biofilms provide enhanced resilience toward antibiotics and the immune response and impose remarkable therapeutic challenges in clinics worldwide. This review provides an overview and an updated perspective on staphylococcal biofilms, describing the characteristic features of biofilm formation, the structural and functional properties of the biofilm matrix, and the most important mechanisms involved in the regulation of staphylococcal biofilm formation. Finally, we highlight promising strategies and technologies, including multitargeted or combinational therapies, to eradicate staphylococcal biofilms.
IMGT/HIGHV-QUEST: THE IMGT® WEB PORTAL FOR IMMUNOGLOBULIN (IG) OR ANTIBODY AND T CELL RECEPTOR (TR) ANALYSIS FROM NGS HIGH THROUGHPUT AND DEEP SEQUENCING

BACKGROUND The number of antigen receptors, immunoglobulins (IG) or antibodies and T cell receptors (TR) of the adaptive immune response in vertebrates with jaws is almost unlimited (2.10 12 per individual in humans). This huge diversity results from complex mechanisms in the synthesis of the variable (V) domains, that include DNA molecular rearrangements of the V, diversity (D) and joining (J) genes, N-diversity at the V-(D)-J junctions and, for IG, somatic hypermutations. The specificity of the V domains is conferred by the complementarity determining regions (CDR) and more particularly the CDR3. IMGT®, the international ImMunoGeneTics information system®, has developed online tools that provide a detailed and accurate sequence analysis of the V domains (IMGT/V-QUEST) and CDR3 (IMGT/JunctionAnalysis), based on IMGT-ONTOLOGY. However online analyses are limited to 50 sequences per batch. The challenge was to provide identical high quality analysis for the huge number of sequences obtained by Next Generation Sequencing (NGS) high throughput and deep sequencing. Results IMGT® has developed IMGT/HighV-QUEST that analyses up to 150,000 IG or TR V domain sequences per batch and performs statistical analysis on the results of up to 450,000 sequences. IMGT/HighV-QUEST provides users with: (i) a friendly web interface for submission and results retrieval, (ii) high quality detailed results of IMGT/V-QUEST and IMGT/JunctionAnalysis, based on the IMGT-ONTOLOGY concepts and IMGT Scientific chart rules, (iii) a standardized frame for NGS statistical analysis, based on ‘Results category’ (‘1 copy’, ‘More than 1’, ‘single allele’, ‘several alleles (or genes)’, (iv) detailed standardized statistical analysis tables and histograms (e.g., V, D and J usage, CDR3-IMGT lengths). Conclusions
Hidradenitis suppurativa and psychiatric comorbidities, suicides and substance abuse: systematic review and meta-analysis

Background Hidradenitis suppurativa (HS) is a chronic inflammatory skin disorder of the hair follicles, and has been associated with a multitude of systemic disorders and pathologies. There is increasing evidence to suggest that chronic inflammatory skin disorders may be associated with psychiatric comorbidities, however this relationship has not been well established. We aimed perform a systematic review and meta-analysis to assess the association between HS and psychiatric comorbidities, suicide and substance abuse. Methods A systematic review and meta-analysis was performed according to PRISMA guidelines. Results HS cases had a significantly higher odds of having schizophrenia compared to the control group (OR 1.66, 95% CI: 1.53–1.79, P<0.00001). There was also a significant association with bipolar disorders (OR 1.96,95% CI: 1.65–2.33, P<0.00001), depression (OR 1.75, 95% CI: 1.44–2.13, P<0.00001), anxiety (OR 1.71, 95% CI: 1.51–1.92, P<0.00001), and personality disorders (OR 1.50, 95% CI: 1.18–1.92, P=0.001), suicide (OR 2.08, 95% CI: 1.27–3.42, P=0.004), substance-related disorders (OR 2.84, 95% CI: 2.33–3.46, P<0.00001), and alcohol abuse (OR 1.94, 95% CI: 1.43–2.64, P<0.0001). Conclusions For dermatologists treating patients with HS, screening for these comorbidities, psychiatric referral and adequately managing pain will improve the overall wellbeing of patients.
Should personal practice be part of cognitive behaviour therapy training? Results from two self-practice/self-reflection cohort control pilot studies.

There are good theoretical and empirical grounds to suggest that personal practices (PPs) (e.g. self-practice/self-reflection programs, meditation programs, personal therapy) can have a positive impact on therapist skills and client outcomes. However, to date, a weakness in many PP studies is the lack of cohort control groups. The two pilot studies reported in this paper examined self-practice/self-reflection (SP/SR) programs integrated into postgraduate psychology training and are the first to include cohort control groups. Study 1 compared outcomes of students assigned to either SP/SR (n = 17) or a cognitive-behaviour therapy (CBT) book study group (n = 13) during their first clinical placement. Study 2 compared outcomes of students who completed the SP/SR program as part of CBT training (n = 12) with participants who completed the same CBT training in the previous year without an SP/SR program (n = 17). Significant improvements in therapist confidence for the SP/SR groups were found in both studies. Study 2 also showed significantly higher therapist self-awareness and lower burn-out scores in the SP/SR group. These studies are limited by their small sample size and the lack of random allocation. Nevertheless, they provide preliminary empirical evidence demonstrating large effects of PP on trainees' personal and therapist selves, and offers a basis for further research using randomized controlled designs with larger sample sizes.
Understanding the Role of Innate Immune Cells and Identifying Genes in Breast Cancer Microenvironment

The innate immune system is the first line of defense against invading pathogens and has a major role in clearing transformed cells, besides its essential role in activating the adaptive immune system. Macrophages, dendritic cells, NK cells, and granulocytes are part of the innate immune system that accumulate in the tumor microenvironment such as breast cancer. These cells induce inflammation in situ by secreting cytokines and chemokines that promote tumor growth and progression, in addition to orchestrating the activities of other immune cells. In breast cancer microenvironment, innate immune cells are skewed towards immunosuppression that may lead to tumor evasion. However, the mechanisms by which immune cells could interact with breast cancer cells are complex and not fully understood. Therefore, the importance of the mammary tumor microenvironment in the development, growth, and progression of cancer is widely recognized. With the advances of using bioinformatics and analyzing data from gene banks, several genes involved in NK cells of breast cancer individuals have been identified. In this review, we discuss the activities of certain genes involved in the cross-talk among NK cells and breast cancer. Consequently, altering tumor immune microenvironment can make breast tumors more responsive to immunotherapy.
Epithelial Cell Migration and Proliferation Patterns During Initial Wound Closure in Normal Mice and an Experimental Model of Limbal Stem Cell Deficiency

Purpose Establishing the dynamics of corneal wound healing is of vital importance to better understand corneal inflammation, pathology, and corneal regeneration. Numerous studies have made great strides in investigating multiple aspects of corneal wound healing; however, some aspects remain to be elucidated. This study worked toward establishing (1) if epithelial limbal stem cells (LSCs) are necessary for healing all corneal wounds, (2) the mechanism by which epithelial cells migrate toward the wound, and (3) if centrifugal epithelial cell movement exists. Methods To establish different aspects of corneal epithelial wound healing we subjected mice lacking hyaluronan synthase 2 (previously shown to lack LSCs) and wild-type mice to different corneal debridement injury models. Results Our data show that both LSCs and corneal epithelial cells contribute toward closure of corneal wounds. In wild-type mice, removal of the limbal rim delayed closure of 1.5-mm wounds, and not of 0.75-mm wounds, indicating that smaller wounds do not rely on LSCs as do larger wounds. In mice shown to lack LSCs, removal of the limbal rim did not affect wound healing, irrespective of the wound size. Finally, transient amplifying cells and central epithelial cells move toward a central corneal wound in a centripetal manner, whereas central epithelial cells may move in a centrifugal manner to resurface peripheral corneal wounds. Conclusions Our findings show the dimensions of the corneal wound dictate involvement of LSCs. Our data suggest that divergent findings by different groups on the dynamics of wound healing can be in part owing to differences in the wounding models used.
Laparoscopic anterior resection for rectal stenosis caused by ALTA injection for internal hemorrhoids: A case report

We herein report the first case of rectal stenosis that developed after internal hemorrhoid treatment with aluminum potassium sulfate and tannic acid (ALTA) therapy that was successfully treated by laparoscopic surgery. A 72‐year‐old man suffered from a fever and rectal stenosis after undergoing internal hemorrhoid treatment with a submucosal injection of ALTA at a previous clinic. Three months after ALTA therapy, he developed frequent mucous and bloody stools. Lower intestinal tract endoscopy revealed circumferential severe rectal stenosis. He was therefore referred to our hospital. The patient suffered from frequent stool build‐up and difficulty defecating. We performed balloon‐dilatation intervention. The stenosis was not improved at all. Five months after ALTA therapy, we performed laparoscopic low anterior resection with diverting ileostomy. Three months after the operation, ileostomy takedown was performed. The patient has experienced no rectal stenosis in the 2 years since his radical operation.
Laminin-coated multifilament entubulation, combined with Schwann cells and glial cell line-derived neurotrophic factor, promotes unidirectional axonal regeneration in a rat model of thoracic spinal cord hemisection

Biomaterial bridging provides physical substrates to guide axonal growth across the lesion. To achieve efficient directional guidance, combinatory strategies using permissive matrix, cells and trophic factors are necessary. In the present study, we evaluated permissive effect of poly (acrylonitrile-co-vinyl chloride) guidance channels filled by different densities of laminin-precoated unidirectional polypropylene filaments combined with Schwann cells, and glial cell line-derived neurotrophic factor for axonal regeneration through a T10 hemisected spinal cord gap in adult rats. We found that channels with filaments significantly reduced the lesion cavity, astrocytic gliosis, and inflammatory responses at the graft-host boundaries. The laminin coated low density filament provided the most favorable directional guidance for axonal regeneration which was enhanced by co-grafting of Schwann cells and glial cell line-derived neurotrophic factor. These results demonstrate that the combinatorial strategy of filament-filled guiding scaffold, adhesive molecular laminin, Schwann cells, and glial cell line-derived neurotrophic factor, provides optimal topographical cues in stimulating directional axonal regeneration following spinal cord injury. This study was approved by Indiana University Institutional Animal Care and Use Committees (IACUC #:11011) on October 29, 2015.
Unveiling the Risk Period for Death After Respiratory Syncytial Virus Illness in Young Children Using a Self-Controlled Case Series Design.

BACKGROUND Respiratory syncytial virus (RSV)-related acute lower respiratory infection is an important cause of death in infants and young children. However, little is known about the risk period for RSV-related deaths after presentation to health services with an RSV illness. METHODS Using the Scottish national mortality database, we identified deaths from respiratory/circulatory causes (hereafter "respiratory/circulatory deaths") in young children aged <5 years during 2009-2016, whose medical history and records of laboratory-confirmed RSV infections were obtained by linking the mortality database to the national surveillance data set and the Scottish Morbidity Record. We used a self-controlled case series (SCCS) design to evaluate the relative incidence of deaths with respiratory/circulatory deaths in the first year after an RSV episode. We defined the risk interval as the first year after the RSV episode, and the control interval as the period before and after the risk interval until 5 years after birth. Age-adjusted incidence ratio and attributable fraction were generated using the R software package SCCS. RESULTS We included 162 respiratory/circulatory deaths, of which 36 occurred in children with a history of laboratory-confirmed RSV infection. We found that the mortality risk decreased with time after the RSV episode and that the risk was statistically significant for the month after RSV illness. More than 90% of respiratory/circulatory deaths occurring within 1 week after the RSV episode were attributable to RSV (attributable fraction, 93.9%; 95% confidence interval, 77.6%-98.4%), compared with about 80% of those occurring 1 week to 1 month after RSV illness (80.3%; 28.5%-94.6%). CONCLUSIONS We found an increased risk of death in the first month after an RSV illness episode leading to healthcare attendance. This provides a practical cutoff time window for community-based surveillance studies estimating RSV-related mortality risk. Further studies are warranted to assess the mortality risk beyond the first month after RSV illness episode.
Turgor - a limiting factor for radial growth in mature conifers along an elevational gradient.

A valid representation of intra-annual wood-formation processes in global vegetation models is vital for assessing climate change impacts on the forest carbon stock. Yet, wood formation is generally modelled with photosynthesis, despite mounting evidence that cambial activity is rather directly constrained by limiting environmental factors. Here, we apply a state-of-the-art turgor-driven growth model to simulate four years of hourly stem radial increment from Picea abies (L.) Karst. and Larix decidua Mill. growing along an elevational gradient. For the first time, wood formation observations were used to validate weekly to annual stem radial increment simulations, while environmental measurements were used to assess the climatic constraints on turgor-driven growth. Model simulations matched the observed timing and dynamics of wood formation. Using the detailed model outputs, we identified a strict environmental regulation on stem growth (air temperature >2 °C and soil water potential >-0.6 MPa). Warmer and drier summers reduced the growth rate due to turgor limitation despite warmer temperatures being favourable for cambial activity. These findings suggest that turgor is a central driver of the forest carbon sink and should be considered in next-generation vegetation models, particularly in the context of global warming and increasing frequency of droughts.