Structure and phase transitions in niobium and tantalum derived nanoscale transition metal perovskites, Ba(Ti,MV)O3, M=Nb,Ta.

The prospect of creating ferroelectric or high permittivity nanomaterials provides motivation for investigating complex transition metal oxides of the form Ba(Ti, MV)O3, where M = Nb or Ta. Solid state processing typically produces mixtures of crystalline phases, rarely beyond minimally doped Nb/Ta. Using a modified sol-gel method, we prepared single phase nanocrystals of Ba(Ti, M)O3. Compositional and elemental analysis puts the empirical formulas close to BaTi0.5Nb0.5O3-δ and BaTi0.5Ta0.5O3-δ. For both materials, a reversible temperature dependent phase transition (non-centrosymmetric to symmetric) is observed in the Raman spectrum in the region 533-583 K (260-310 °C); for Ba(Ti, Nb)O3, the onset is at 543 K (270 °C); and for Ba(Ti, Ta)O3, the onset is at 533 K (260 °C), which are comparable with 390-393 K (117-120 °C) for bulk BaTiO3. The crystal structure was resolved by examination of the powder x-ray diffraction and atomic pair distribution function (PDF) analysis of synchrotron total scattering data. It was postulated whether the structure adopted at the nanoscale was single or double perovskite. Double perovskites (A2B'B″O6) are characterized by the type and extent of cation ordering, which gives rise to higher symmetry crystal structures. PDF analysis was used to examine all likely candidate structures and to look for evidence of higher symmetry. The feasible phase space that evolves includes the ordered double perovskite structure Ba2(Ti, MV)O6 (M = Nb, Ta) Fm-3m, a disordered cubic structure, as a suitable high temperature analog, Ba(Ti, MV)O3Pm-3m, and an orthorhombic Ba(Ti, MV)O3Amm2, a room temperature structure that presents an unusually high level of lattice displacement, possibly due to octahedral tilting, and indication of a highly polarized crystal.

Drain-site recurrence of an ileocaecal valve adenocarcinoma.

Drain-site recurrence following colorectal cancer resection is a rare event and is described in few case reports. The majority of these reports are following minimally invasive surgery. This report describes a case of an isolated drain-site recurrence of primary colorectal cancer in a male patient in his 50s. He previously underwent an open right hemicolectomy and segmental small bowel resection for an obstructing ileocaecal valve adenocarcinoma. This was followed by adjuvant chemotherapy. Two years into surveillance, a redo ileocolic resection was performed for an anastomotic recurrence. While undergoing surveillance imaging, a new deposit was detected at a right-sided surgical drain site. Subsequently, a full thickness en bloc resection was performed. To date, the postoperative course has been uneventful. This case describes a drain-site recurrence from a colorectal primary.

IL11-mediated stromal cell activation may not be the master regulator of pro-fibrotic signaling downstream of TGFß.

Fibrotic diseases, such as idiopathic pulmonary fibrosis (IPF) and systemic scleroderma (SSc), are commonly associated with high morbidity and mortality, thereby representing a significant unmet medical need. Interleukin 11 (IL11)-mediated cell activation has been identified as a central mechanism for promoting fibrosis downstream of TGFß. IL11 signaling has recently been reported to promote fibroblast-to-myofibroblast transition, thus leading to various pro-fibrotic phenotypic changes. We confirmed increased mRNA expression of IL11 and IL11Rα in fibrotic diseases by OMICs approaches and in situ hybridization. However, the vital role of IL11 as a driver for fibrosis was not recapitulated. While induction of IL11 secretion was observed downstream of TGFß signaling in human lung fibroblasts and epithelial cells, the cellular responses induced by IL11 was quantitatively and qualitatively inferior to that of TGFß at the transcriptional and translational levels. IL11 blocking antibodies inhibited IL11Rα-proximal STAT3 activation but failed to block TGFß-induced profibrotic signals. In summary, our results challenge the concept of IL11 blockade as a strategy for providing transformative treatment for fibrosis.

Single-haplotype comparative genomics provides insights into lineage-specific structural variation during cat evolution.

The role of structurally dynamic genomic regions in speciation is poorly understood due to challenges inherent in diploid genome assembly. Here we reconstructed the evolutionary dynamics of structural variation in five cat species by phasing the genomes of three interspecies F1 hybrids to generate near-gapless single-haplotype assemblies. We discerned that cat genomes have a paucity of segmental duplications relative to great apes, explaining their remarkable karyotypic stability. X chromosomes were hotspots of structural variation, including enrichment with inversions in a large recombination desert with characteristics of a supergene. The X-linked macrosatellite DXZ4 evolves more rapidly than 99.5% of the genome clarifying its role in felid hybrid incompatibility. Resolved sensory gene repertoires revealed functional copy number changes associated with ecomorphological adaptations, sociality and domestication. This study highlights the value of gapless genomes to reveal structural mechanisms underpinning karyotypic evolution, reproductive isolation and ecological niche adaptation.

A novel video compendium of real surgical patient interactions for medical students.

Objective: To develop a novel video compendium of real surgical patient interactions as a tool for medical student education and to evaluate our institutional experience of its usefulness. Design: Prospective development of a video compendium of real surgical patient interactions. Setting: Single university affiliated hospital in Cork, Ireland. Participants: Patients with illnesses relevant to the surgery curriculum and students from an Irish medical school. Results: Videos were recorded of the clinical interaction between a consultant surgeon and patients, capturing focused history taking and/or clinical examination, with an associated set of explanatory notes. Fifty videos were developed with a tiered release to the clinical year medical students, via their virtual learning/education platform. Three hundred and eleven students responded to the questionnaire across 3-student year groups (311/585-53 %). Fifty-two percent of students did not have their clinical rotations affected by the COVID-19 pandemic. >90 % of students agreed that the videos helped history taking and clinical examination technique. >80 % of students agreed that the accompanying text slides reinforced key points and helped with understanding difficult topics. Eighty-five percent of students reported that the videos increased exposure to surgical patients and pathology. Eighty-five percent of students rated their experience as at least 4 out of 5. Conclusions: This online educational compendium bridged a gap for students with limited clinical exposure during the COVID-19 pandemic, and has become an important resource for all clinical students. Our novel engagement with real patients sets this compendium apart from resources which use actors.

Ancient DNA reveals genetic admixture in China during tiger evolution.

The tiger (Panthera tigris) is a charismatic megafauna species that originated and diversified in Asia and probably experienced population contraction and expansion during the Pleistocene, resulting in low genetic diversity of modern tigers. However, little is known about patterns of genomic diversity in ancient populations. Here we generated whole-genome sequences from ancient or historical (100-10,000 yr old) specimens collected across mainland Asia, including a 10,600-yr-old Russian Far East specimen (RUSA21, 8× coverage) plus six ancient mitogenomes, 14 South China tigers (0.1-12×) and three Caspian tigers (4-8×). Admixture analysis showed that RUSA21 clustered within modern Northeast Asian phylogroups and partially derived from an extinct Late Pleistocene lineage. While some of the 8,000-10,000-yr-old Russian Far East mitogenomes are basal to all tigers, one 2,000-yr-old specimen resembles present Amur tigers. Phylogenomic analyses suggested that the Caspian tiger probably dispersed from an ancestral Northeast Asian population and experienced gene flow from southern Bengal tigers. Lastly, genome-wide monophyly supported the South China tiger as a distinct subspecies, albeit with mitochondrial paraphyly, hence resolving its longstanding taxonomic controversy. The distribution of mitochondrial haplogroups corroborated by biogeographical modelling suggested that Southwest China was a Late Pleistocene refugium for a relic basal lineage. As suitable habitat returned, admixture between divergent lineages of South China tigers took place in Eastern China, promoting the evolution of other northern subspecies. Altogether, our analysis of ancient genomes sheds light on the evolutionary history of tigers and supports the existence of nine modern subspecies.

Validation of a Custom Interface Pressure Measurement System to Improve Fitting of Transtibial Prosthetic Check Sockets.

Achievement of fit between the residual limb and prosthetic socket during socket manufacture is a priority for clinicians and is essential for safety. Clinicians have recognised the potential benefits of having a sensor system that can provide objective socket-limb interface pressure measurements during socket fitting, but the cost of existing systems makes current technology prohibitive. This study will report on the characterisation, validation and preliminary clinical implementation of a low cost, portable, wireless sensor system designed for use during socket manufacture. Characterisation and benchtop testing demonstrated acceptable accuracy, behaviour at variable temperature, and dynamic response for use in prosthetic socket applications. Our sensor system was validated with simultaneous measurement by a commercial sensor system in the sockets of three transtibial prosthesis users during a fitting session in the clinic. There were no statistically significant differences between the sensor system and the commercial sensor for a variety of functional activities. The sensor system was found to be valid in this clinical context. Future work should explore how pressure data relates to ratings of fit and comfort, and how objective pressure data might be used to assist in clinical decision making.

Chromosome-length genome assemblies and cytogenomic analyses of pangolins reveal remarkable chromosome counts and plasticity.

We report the first chromosome-length genome assemblies for three species in the mammalian order Pholidota: the white-bellied, Chinese, and Sunda pangolins. Surprisingly, we observe extraordinary karyotypic plasticity within this order and, in female white-bellied pangolins, the largest number of chromosomes reported in a Laurasiatherian mammal: 2n = 114. We perform the first karyotype analysis of an African pangolin and report a Y-autosome fusion in white-bellied pangolins, resulting in 2n = 113 for males. We employ a novel strategy to confirm the fusion and identify the autosome involved by finding the pseudoautosomal region (PAR) in the female genome assembly and analyzing the 3D contact frequency between PAR sequences and the rest of the genome in male and female white-bellied pangolins. Analyses of genetic variability show that white-bellied pangolins have intermediate levels of genome-wide heterozygosity relative to Chinese and Sunda pangolins, consistent with two moderate declines of historical effective population size. Our results reveal a remarkable feature of pangolin genome biology and highlight the need for further studies of these unique and endangered mammals.

Temporal increase in the incidence of anal squamous cell carcinoma in Kentucky and factors associated with adverse outcomes.

BACKGROUND: Anal squamous cell cancer (ASCC) incidence in Kentucky is increasing at an alarming rate. In 2009, the incidence surpassed the US national average (2.66 vs. 1.77/100,000 people), and currently, Kentucky ranks second by state per capita. The reasons for this rise are unclear. We hypothesize individuals with ASCC in Kentucky have some unique risk factors associated with worse outcomes. METHODS: Individuals with ASCC in a population-level state database (1995-2016), as well as those treated at two urban university-affiliated tertiary care centers (2011-2018), were included and analyzed separately. We evaluated patient-level factors including demographics, tobacco use, stage of disease, HIV-status, and HPV-type. We evaluated factors associated with treatment and survival using univariable and multivariable survival analyses. RESULTS: There were 1698 individuals in state data and 101 in urban center data. In the urban cohort, 77% of patients were ever-smokers. Eighty-four percent of patients had positive HPV testing, and 58% were positive for HPV 16. Seventy-two percent of patients were positive for p16. Neither smoking, HPV, nor p16 status were associated with disease persistence, recurrence-free survival, or overall survival (all p > 0.05). Poorly controlled HIV (CD4 count <500) at time of ASCC diagnosis was associated disease persistence (p = 0.032). Stage III disease (adjusted HR = 5.25, p = 0.025) and local excision (relative to chemoradiation; aHR = 0.19, p = 0.017) were significantly associated with reduced recurrence-free survival. CONCLUSIONS: The rate of ASCC in Kentucky has doubled over the last 10 years, which is outpacing anal SCC rates in the US with the most dramatic rates seen in Kentucky women. The underlying reasons for this are unclear and require further study. There may be other risk factors unique to Kentucky.

Arthroscopic Subdeltoid Transfer of the Long Head of the Biceps Tendon to the Conjoint Tendon.

Surgical intervention is often recommended for refractory pathology affecting the biceps-labrum complex. Tenodesis of the long head of the biceps tendon (LHBT) is a widely accepted treatment modality; however, the optimal technique remains elusive. Arthroscopic subdeltoid transfer of the LHBT to the conjoint tendon, as described in this technical note, continues to demonstrate excellent clinical results. Its advantages include soft tissue-to-soft tissue healing, an advantageous biomechanical construct, and comprehensive evaluation and decompression of the LHBT including the extra-articular bicipital tunnel. The primary limitation of this procedure is the perceived learning curve for safe navigation within the subdeltoid space.

Whole genome sequencing reveals population diversity and variation in HIV-1 specific host genes.

HIV infection continues to be a major global public health issue. The population heterogeneity in susceptibility or resistance to HIV-1 and progression upon infection is attributable to, among other factors, host genetic variation. Therefore, identifying population-specific variation and genetic modifiers of HIV infectivity can catapult the invention of effective strategies against HIV-1 in African populations. Here, we investigated whole genome sequences of 390 unrelated HIV-positive and -negative individuals from Botswana. We report 27.7 million single nucleotide variations (SNVs) in the complete genomes of Botswana nationals, of which 2.8 million were missing in public databases. Our population structure analysis revealed a largely homogenous structure in the Botswana population. Admixture analysis showed elevated components shared between the Botswana population and the Niger-Congo (65.9%), Khoe-San (32.9%), and Europeans (1.1%) ancestries in the population of Botswana. Statistical significance of the mutational burden of deleterious and loss-of-function variants per gene against a null model was estimated. The most deleterious variants were enriched in five genes: ACTRT2 (the Actin Related Protein T2), HOXD12 (homeobox D12), ABCB5 (ATP binding cassette subfamily B member 5), ATP8B4 (ATPase phospholipid transporting 8B4) and ABCC12 (ATP Binding Cassette Subfamily C Member 12). These genes are enriched in the glycolysis and gluconeogenesis (p < 2.84e-6) pathways and therefore, may contribute to the emerging field of immunometabolism in which therapy against HIV-1 infection is being evaluated. Published transcriptomic evidence supports the role of the glycolysis/gluconeogenesis pathways in the regulation of susceptibility to HIV, and that cumulative effects of genetic modifiers in glycolysis/gluconeogenesis pathways may potentially have effects on the expression and clinical variability of HIV-1. Identified genes and pathways provide novel avenues for other interventions, with the potential for informing the design of new therapeutics.

Large-bowel obstruction secondary to Enterobius vermicularis pseudotumour.

Enterobius vermicularis infection is typically observed in paediatric patients and manifests with perianal pruritus, but other manifestations or ectopic presentations have been reported in the literature. We present the case of a man in his 60ss with a large-bowel obstruction with symptoms including a 4-day history of progressive abdominal pain, distension, vomiting and absolute constipation. On examination, his abdomen was distended with tinkling bowel sounds on auscultation. Cross-sectional imaging demonstrated an obstructing mass in the distal descending colon. An emergency laparoscopic Hartmann's procedure was performed and the patient made an uneventful recovery. An intraoperative colonoscopy demonstrated numerous white threadworms in the colon. Histological analysis demonstrated a pseudotumour related to Enterobius vermicularis infection. This case represents a rare differential diagnosis for a large-bowel obstruction.

The Pioneer Advantage: Filling the blank spots on the map of genome diversity in Europe.

Documenting genome diversity is important for the local biomedical communities and instrumental in developing precision and personalized medicine. Currently, tens of thousands of whole-genome sequences from Europe are publicly available, but most of these represent populations of developed countries of Europe. The uneven distribution of the available data is further impaired by the lack of data sharing. Recent whole-genome studies in Eastern Europe, one in Ukraine and one in Russia, demonstrated that local genome diversity and population structure from Eastern Europe historically had not been fully represented. An unexpected wealth of genomic variation uncovered in these studies was not so much a consequence of high variation within their population, but rather due to the "pioneer advantage." We discovered more variants because we were the first to prospect in the Eastern European genome pool. This simple comparison underscores the importance of removing the remaining geographic genome deserts from the rest of the world map of the human genome diversity.

Should We Be Screening for Ischaemic Heart Disease Earlier in Childhood?

Ischaemic heart disease is the most common cause of death in males and the second in the female gender. Yet we often only focus on identification and treatment of this foremost cause of death in adulthood. The review asks the question what form of coronary disease do we encounter in childhood, what predisposing factors give rise to atherosclerosis and what strategies in childhood could we employ to detect and reduce atherosclerosis development in later life.

Design and Development of a Bimodal Optical Instrument for Simultaneous Vibrational Spectroscopy Measurements.

Vibrational spectroscopy techniques are widely used in analytical chemistry, physics and biology. The most prominent techniques are Raman and Fourier-transform infrared spectroscopy (FTIR). Combining both techniques delivers complementary information of the test sample. We present the design, construction, and calibration of a novel bimodal spectroscopy system featuring both Raman and infrared measurements simultaneously on the same sample without mutual interference. The optomechanical design provides a modular flexible system for solid and liquid samples and different configurations for Raman. As a novel feature, the Raman module can be operated off-axis for optical sectioning. The calibrated system demonstrates high sensitivity, precision, and resolution for simultaneous operation of both techniques and shows excellent calibration curves with coefficients of determination greater than 0.96. We demonstrate the ability to simultaneously measure Raman and infrared spectra of complex biological material using bovine serum albumin. The performance competes with commercial systems; moreover, it presents the additional advantage of simultaneously operating Raman and infrared techniques. To the best of our knowledge, it is the first demonstration of a combined Raman-infrared system that can analyze the same sample volume and obtain optically sectioned Raman signals. Additionally, quantitative comparison of confocality of backscattering micro-Raman and off-axis Raman was performed for the first time.

A decade of GigaScience: A perspective on conservation genetics.

Wide interest in species conservation is young. To many it began early in 1903 when Teddy Roosevelt and John Muir set up a camp under the Grizzly Giant in the Mariposa Grove of California's Yosemite Valley. Over three days they decided to broaden the US National Park footprint across the USA. Conservationists were inspired in the coming decades by the writings of wildlife conservation pioneers-Osa Johnson (I Married Adventure), Karen Blixen (Out of Africa) and Rachel Carson (The Silent Spring). Countless crusaders developed a passion for preserving dwindling species in those early days, yet none of these conservation advocates mentioned the word genetics, let alone genomics. The genome sequencing projects that have followed on from these have brought in an enormous amount of data, including whole genome sequences for thousands of non-human species, both individual and population wide. This huge resource has revolutionized conservation genetics, bringing in ways to assess the health of at-risk populations, devise genetic-driven breeding strategies, and other means to attempt to preserve the over 1 million species (and growing) under threat today.

Room Temperature Fabrication of Macroporous Lignin Membranes for the Scalable Production of Black Silicon.

Rising global demand for biodegradable materials and green sources of energy has brought attention to lignin. Herein, we report a method for manufacturing standalone lignin membranes without additives for the first time to date. We demonstrate a scalable method for macroporous (∼100 to 200 nm pores) lignin membrane production using four different organosolv lignin materials under a humid environment (>50% relative humidity) at ambient temperatures (∼20 °C). A range of different thicknesses is reported with densely porous films observed to form if the membrane thickness is below 100 nm. The fabricated membranes were readily used as a template for Ni2+ incorporation to produce a nickel oxide membrane after UV/ozone treatment. The resultant mask was etched via an inductively coupled plasma reactive ion etch process, forming a silicon membrane and as a result yielding black silicon (BSi) with a pore depth of >1 µm after 3 min with reflectance <3% in the visible light region. We anticipate that our lignin membrane methodology can be readily applied to various processes ranging from catalysis to sensing and adapted to large-scale manufacturing.

Impact of myopenia and myosteatosis in patients undergoing abdominal surgery for chronic pancreatitis.

BACKGROUND: Surgery for chronic pancreatitis is associated with major morbidity and mortality. The aim of this study is to examine the role of preoperative muscle volume and quality on postoperative outcomes in patients with chronic pancreatitis. METHODS: All patients who underwent abdominal surgery for chronic pancreatitis between 2011 and 2018 were identified from an institutional surgical database. Patient demographics, clinical indices, and perioperative computed tomography scans were collected. Myopenia and myosteatosis were measured at the L3 vertebral level. Regression analysis was used to identify risk factors for major complications (Clavien-Dindo ≥3a) and length of stay. RESULTS: Seventy-five patients were identified. Toxic-metabolic or obstructive causes were the main underlying etiologies. Thirty patients were myopenic (40%), and 36 patients were myosteatotic (48%). Sixteen patients (21%) had a major complication. Median length of stay was 10 days. Both myopenia and myosteatosis were associated with major complications (hazard ratio = 7.85, 95% confidence interval: 1.91-32.29, P = .004 and hazard ratio = 4.351, 95% confidence interval: 1.22-15.52, P = .023). Myosteatosis was associated with increased length of stay (parameter estimate = 0.297, 95% confidence interval: 0.012-0.583, P = .041). CONCLUSION: Myopenia and myosteatosis were common and significant risk factors for adverse postoperative events. Preoperative muscle assessment may help in the risk stratification of surgical patients and identify patients that require preoperative nutritional and physical optimization.