Phase Diagrams of Alloys and Their Hydrides via On-Lattice Graph Neural Networks and Limited Training Data.

Efficient prediction of sampling-intensive thermodynamic properties is needed to evaluate material performance and permit high-throughput materials modeling for a diverse array of technology applications. To alleviate the prohibitive computational expense of high-throughput configurational sampling with density functional theory (DFT), surrogate modeling strategies like cluster expansion are many orders of magnitude more efficient but can be difficult to construct in systems with high compositional complexity. We therefore employ minimal-complexity graph neural network models that accurately predict and can even extrapolate to out-of-train distribution formation energies of DFT-relaxed structures from an ideal (unrelaxed) crystallographic representation.

A framework to validate fluorescently labeled DNA-binding proteins for single-molecule experiments.

Due to the enhanced labeling capability of maleimide-based fluorescent probes, lysine-cysteine-lysine (KCK) tags are frequently added to proteins for visualization. In this study, we employed an in vitro single-molecule DNA flow-stretching assay as a sensitive way to assess the impact of the KCK tag on the property of DNA-binding proteins. Using Bacillus subtilis ParB as an example, we show that, although no noticeable changes were detected by in vivo fluorescence imaging and chromatin immunoprecipitation (ChIP) assays, the KCK tag substantially altered ParB's DNA compaction rates and its response to nucleotide binding and to the presence of the specific sequence (parS) on the DNA.

Using DNA flow-stretching assay as a tool to validate the tagging of DNA-binding proteins for single-molecule experiments.

Due to the enhanced labeling capability of maleimide-based fluorescent probes, lysine-cysteine-lysine (KCK) tags are frequently added to proteins for visualization. In this study, we employed single-molecule DNA flow-stretching assay as a sensitive way to assess the impact of the KCK-tag on the property of DNA-binding proteins. Using ParB as an example, we show that, although no noticeable changes were detected by fluorescence imaging and chromatin immunoprecipitation (ChIP) assays, the KCK-tag substantially altered ParB's DNA compaction rates, its response to nucleotide binding and to the presence of the specific sequence () on the DNA.

The utility of limited Spanish proficiency in interpreted genetic counseling sessions.

Professional interpreters are an integral component of healthcare for Spanish-speaking individuals with limited English proficiency (LEP). Research has demonstrated that errors in interpretation are common and can contribute to poor outcomes for Spanish-speaking clients. Providers with some Spanish proficiency may be able to detect clinically significant interpretation errors, potentially limiting negative clinical outcomes and helping to reduce health disparities for clients with LEP.

Next-generation sequencing of a combinatorial peptide phage library screened against ubiquitin identifies peptide aptamers that can inhibit the ubiquitin transfer cascade.

Defining dynamic protein-protein interactions in the ubiquitin conjugation reaction is a challenging research area. Generating peptide aptamers that target components such as ubiquitin itself, E1, E2, or E3 could provide tools to dissect novel features of the enzymatic cascade. Next-generation deep sequencing platforms were used to identify peptide sequences isolated from phage-peptide libraries screened against Ubiquitin and its ortholog NEDD8.

Cephalomedullary blade cut-ins: a poorly understood phenomenon.

Objectives: Proximal femoral nail antirotation (PFNA) cut-in is a unique phenomenon seen in pertrochanteric hip fractures treated with the PFNA. Cut-in refers to the superomedial migration of the proximal femoral blade into the femoral head and hip joint. We recognize that cut-in is a completely separate entity from the well-described cut-out failure.

Discovering Putative Protein Targets of Small Molecules: A Study of the p53 Activator Nutlin.

Small molecule drugs bind to a pocket in disease causing target proteins based on complementarity in shape and physicochemical properties. There is a likelihood that other proteins could have binding sites that are structurally similar to the target protein. Binding to these other proteins could alter their activities leading to off target effects of the drug.

Chemoresistance of cancer floating cells is independent of their ability to form 3D structures: Implications for anticancer drug screening.

Three-dimensional (3D) culture systems such as floating spheroids (FSs) and floating tumorspheres (FTs) are widely used as tumor models of chemoresistance. FTs are considered to be enriched in cancer stem-like cells (CS-LCs). In this study, we used cancer cell lines (lung H460, prostate LnCAP, and breast MCF-7) able to form FSs under anchorage-independent conditions and compared with cell lines (prostate PC3 and breast MDA-MB-231) that cannot form FSs under similar conditions.

Developmental validation of the MiSeq FGx Forensic Genomics System for Targeted Next Generation Sequencing in Forensic DNA Casework and Database Laboratories.

Human DNA profiling using PCR at polymorphic short tandem repeat (STR) loci followed by capillary electrophoresis (CE) size separation and length-based allele typing has been the standard in the forensic community for over 20 years. Over the last decade, Next-Generation Sequencing (NGS) matured rapidly, bringing modern advantages to forensic DNA analysis. The MiSeq FGx™ Forensic Genomics System, comprised of the ForenSeq™ DNA Signature Prep Kit, MiSeq FGx™ Reagent Kit, MiSeq FGx™ instrument and ForenSeq™ Universal Analysis Software, uses PCR to simultaneously amplify up to 231 forensic loci in a single multiplex reaction.

Rearrangement of mitochondrial pyruvate dehydrogenase subunit dihydrolipoamide dehydrogenase protein-protein interactions by the MDM2 ligand nutlin-3.

Drugs targeting MDM2's hydrophobic pocket activate p53. However, these agents act allosterically and have agonist effects on MDM2's protein interaction landscape. Dominant p53-independent MDM2-drug responsive-binding proteins have not been stratified.

Determination and validation of volume to be instilled for standardized intra-abdominal pressure measurement in dogs.

Objectives: The objectives of this study were to determine (1) most appropriate volume of saline to be infused into the bladder prior to intra-abdominal pressure (IAP) measurement, (2) to determine if a difference exists between IAP measurements before and after abdominal surgery, and (3) to assess the variability in IAP measurements associated with different saline volumes.

Design: Prospective study.

Setting: University teaching hospital.

A systems wide mass spectrometric based linear motif screen to identify dominant in-vivo interacting proteins for the ubiquitin ligase MDM2.

Linear motifs mediate protein-protein interactions (PPI) that allow expansion of a target protein interactome at a systems level. This study uses a proteomics approach and linear motif sub-stratifications to expand on PPIs of MDM2. MDM2 is a multi-functional protein with over one hundred known binding partners not stratified by hierarchy or function.

Measuring three-dimensional strain distribution in tendon.

Tendons are tough fibrous tissues that facilitate skeletal movement by transferring muscular force to bone. Studies into the effects of mechanical stress on tendons have shown that these can either accelerate healing or cause tendon injuries depending on the load applied. It is known that local strain magnitude and direction play an important role in tendon remodelling and also failure, and different techniques to study strain distribution have been proposed.

Comparison of routine urinalysis and urine Gram stain for detection of bacteriuria in dogs.

Objective: To determine the utility of performing urine Gram stain for detection of bacteriuria compared to routine urine sediment examination and bacterial aerobic urine culture.

Design: Prospective, observational study.

Setting: University teaching hospital.

The association between body mass index and severe biliary infections: a multivariate analysis.

Background: Obesity has been associated with worse infectious disease outcomes. It is a risk factor for cholesterol gallstones, but little is known about associations between body mass index (BMI) and biliary infections. We studied this using factors associated with biliary infections.

Achieving consensus in pressure ulcer reporting.

Pressure ulcers are considered to be a key quality indicator and healthcare providers in England are required to report local pressure ulcer rates. However, there is a lack of standardisation in reporting due to lack of national guidance. The Tissue Viability Society has sought to develop consensus amongst all concerned parties on the most useful and robust methods of data collection.

Therapeutic amprenavir concentrations in cerebrospinal fluid.

Antiretrovirals that reach higher concentrations in cerebrospinal fluid (CSF) are associated with better control of HIV in CSF and possibly better neurocognitive performance. The objective of this study was to determine whether amprenavir (APV) concentrations in CSF are in the therapeutic range. Individuals were selected based on the use of regimens that included fosamprenavir (FPV), a prodrug of APV, and the availability of stored CSF and matched plasma.

Cytocentrifugation: a convenient and efficient method for seeding tendon-derived cells into monolayer cultures or 3-D tissue engineering scaffolds.

Tendon and ligament injuries are very common, requiring some 200,000 reconstructions per year in the USA. Autografting can be used to repair these but donor tissue is limited and harvesting leads to morbidity at the graft sites. Tissue engineering has been used to grow simple tissues such as skin, cartilage and bone and due to their low vascularity and simple structure, tendons should be ideal candidates for such an approach.

Predictors of long-term outcome after laparoscopic esophagomyotomy and Dor fundoplication for achalasia.

Objective: To identify predictors of long-term outcome of laparoscopic Heller myotomy for achalasia, including predictors of heartburn and recurrent dysphagia, which occasionally develop postoperatively.

Design: Retrospective review using interviews of patients.

Setting: Academic university hospital.

Hypertriglyceridemia in combination antiretroviral-treated HIV-positive individuals: potential impact on HIV sensory polyneuropathy.

Objective: in HIV populations that are aging due to improved longevity with combination antiretroviral therapy (CART), both hypertriglyceridemia (hTRG) and sensory neuropathy have become increasingly common. Sensory neuropathy is associated with substantial long-term disability and frequently requires management with analgesics. Elevated serum triglycerides (TRGs) are associated with an increased risk for sensory neuropathy in diabetes mellitus.

Establishing a transport protocol for the delivery of melanocytes and keratinocytes for the treatment of vitiligo.

We have previously developed a cell delivery and transfer technology for delivering autologous keratinocytes and melanocytes to patients with vitiligo. However, for this technology to benefit many patients geographically distant from the cell culture facility transportation issues need to be overcome. In this study we begin to investigate this by looking at what role surface chemistry and medium supplements, including fetal calf serum, CO₂ gassing, and temperature, play in influencing cell viability.

Total raltegravir concentrations in cerebrospinal fluid exceed the 50-percent inhibitory concentration for wild-type HIV-1.

HIV-associated neurocognitive disorders continue to be common. Antiretrovirals that achieve higher concentrations in cerebrospinal fluid (CSF) are associated with better control of HIV and improved cognition. The objective of this study was to measure total raltegravir (RAL) concentrations in CSF and to compare them with matched concentrations in plasma and in vitro inhibitory concentrations.

Operative reports: form and function.

Hypothesis: Little is known about how closely operative reports reflect what was actually performed during an operation, nor has the construction of operative reports been adequately studied with the aims of clarifying the objectives of those reports and improving their efficacy. We hypothesized that if more attention is paid to the objectives of operative reports, their content will more predictably contain the most relevant information, which might channel thinking in beneficial directions during performance of the operation.

Design: Multivariate analysis of 250 laparoscopic cholecystectomy operative reports (125 uncomplicated and 125 with bile duct injury).

The efficacy of medical team training: improved team performance and decreased operating room delays: a detailed analysis of 4863 cases.

Objectives: Medical team training (MTT) has been touted as a way to improve teamwork and patient safety in the operating room (OR).

Methods: OR personal completed a 1-day intensive MTT training. A standardized briefing/debriefing/perioperative routine was developed, including documentation of OR miscues, delays, and a case score (1-5) assigned by the OR team.

Excellent outcomes of laparoscopic esophagomyotomy for achalasia in patients older than 60 years of age.

Background: The effectiveness of an esophagomyotomy for dysphagia in elderly patients with achalasia has been questioned. This study was designed to provide an answer.

Methods: A total of 162 consecutive patients with achalasia who had a laparoscopic myotomy and Dor fundoplication and who were available for follow-up interview were divided by age: < 60 years (range, 14-59; 118 patients), and ≥ 60 years (range, 60-93; 44 patients).