Vertebrate centromeres in mitosis are functionally bipartite structures stabilized by cohesin.

Centromeres are scaffolds for the assembly of kinetochores that ensure chromosome segregation during cell division. How vertebrate centromeres obtain a three-dimensional structure to accomplish their primary function is unclear. Using super-resolution imaging, capture-C, and polymer modeling, we show that vertebrate centromeres are partitioned by condensins into two subdomains during mitosis. The bipartite structure is found in human, mouse, and chicken cells and is therefore a fundamental feature of vertebrate centromeres. Super-resolution imaging and electron tomography reveal that bipartite centromeres assemble bipartite kinetochores, with each subdomain binding a distinct microtubule bundle. Cohesin links the centromere subdomains, limiting their separation in response to spindle forces and avoiding merotelic kinetochore-spindle attachments. Lagging chromosomes during cancer cell divisions frequently have merotelic attachments in which the centromere subdomains are separated and bioriented. Our work reveals a fundamental aspect of vertebrate centromere biology with implications for understanding the mechanisms that guarantee faithful chromosome segregation.

Convergent genes shape budding yeast pericentromeres.

The three-dimensional architecture of the genome governs its maintenance, expression and transmission. The cohesin protein complex organizes the genome by topologically linking distant loci, and is highly enriched in specialized chromosomal domains surrounding centromeres, called pericentromeres1-6. Here we report the three-dimensional structure of pericentromeres in budding yeast (Saccharomyces cerevisiae) and establish the relationship between genome organization and function. We find that convergent genes mark pericentromere borders and, together with core centromeres, define their structure and function by positioning cohesin. Centromeres load cohesin, and convergent genes at pericentromere borders trap it. Each side of the pericentromere is organized into a looped conformation, with border convergent genes at the base. Microtubule attachment extends a single pericentromere loop, size-limited by convergent genes at its borders. Reorienting genes at borders into a tandem configuration repositions cohesin, enlarges the pericentromere and impairs chromosome biorientation during mitosis. Thus, the linear arrangement of transcriptional units together with targeted cohesin loading shapes pericentromeres into a structure that is competent for chromosome segregation. Our results reveal the architecture of the chromosomal region within which kinetochores are embedded, as well as the restructuring caused by microtubule attachment. Furthermore, we establish a direct, causal relationship between the three-dimensional genome organization of a specific chromosomal domain and cellular function.

Text mining and portal development for gene-specific publications on Alzheimer's disease and other neurodegenerative diseases.

BACKGROUND: Tremendous research efforts have been made in the Alzheimer's disease (AD) field to understand the disease etiology, progression and discover treatments for AD. Many mechanistic hypotheses, therapeutic targets and treatment strategies have been proposed in the last few decades. Reviewing previous work and staying current on this ever-growing body of AD publications is an essential yet difficult task for AD researchers. METHODS: In this study, we designed and implemented a natural language processing (NLP) pipeline to extract gene-specific neurodegenerative disease (ND) -focused information from the PubMed database. The collected publication information was filtered and cleaned to construct AD-related gene-specific publication profiles. Six categories of AD-related information are extracted from the processed publication data: publication trend by year, dementia type occurrence, brain region occurrence, mouse model information, keywords occurrence, and co-occurring genes. A user-friendly web portal is then developed using Django framework to provide gene query functions and data visualizations for the generalized and summarized publication information. RESULTS: By implementing the NLP pipeline, we extracted gene-specific ND-related publication information from the abstracts of the publications in the PubMed database. The results are summarized and visualized through an interactive web query portal. Multiple visualization windows display the ND publication trends, mouse models used, dementia types, involved brain regions, keywords to major AD-related biological processes, and co-occurring genes. Direct links to PubMed sites are provided for all recorded publications on the query result page of the web portal. CONCLUSION: The resulting portal is a valuable tool and data source for quick querying and displaying AD publications tailored to users' interested research areas and gene targets, which is especially convenient for users without informatic mining skills. Our study will not only keep AD field researchers updated with the progress of AD research, assist them in conducting preliminary examinations efficiently, but also offers additional support for hypothesis generation and validation which will contribute significantly to the communication, dissemination, and progress of AD research.

High-Density Glass Scintillators for Proton Radiography-Relative Luminosity, Proton Response, and Spatial Resolution.

Proton radiography is a promising development in proton therapy, and researchers are currently exploring optimal detector materials to construct proton radiography detector arrays. High-density glass scintillators may improve integrating-mode proton radiography detectors by increasing spatial resolution and decreasing detector thickness. We evaluated several new scintillators, activated with europium or terbium, with proton response measurements and Monte Carlo simulations, characterizing relative luminosity, ionization quenching, and proton radiograph spatial resolution. We applied a correction based on Birks's analytical model for ionization quenching. The data demonstrate increased relative luminosity with increased activation element concentration, and higher relative luminosity for samples activated with europium. An increased glass density enables more compact detector geometries and higher spatial resolution. These findings suggest that a tungsten and gadolinium oxide-based glass activated with 4% europium is an ideal scintillator for testing in a full-size proton radiography detector.

In-Situ Measurement of Magnetoelectric Coupling and Strain Transfer in Multiferroic Nanocomposites of CoFe2O4 and Hf0.5Zr0.5O2 with Residual Porosity.

With increasing applications for voltage-controlled magnetism, the need to more fully understand magnetoelectric coupling and strain transfer in nanostructured multiferroic composites has also increased. Here, multiferroic nanocomposites were synthesized using block copolymer templating to create mesoporous cobalt ferrite (CFO), followed by partly filling the pores with ferroelectric zirconium-substituted hafnia (HZO) using atomic layer deposition (ALD) to produce a porous multiferroic composite with enhanced mechanical flexibility. Upon electrical poling of the nanocomposite, we observed large changes in the magnetization. These changes partly relaxed upon removing the electric field, suggesting a strain-mediated mechanism. Both the anisotropic strain transfer from HZO to CFO and the strain relaxation after the field was removed were confirmed using high-resolution X-ray diffraction measurements collected during in-situ poling. The in-situ observation of both anisotropic strain transfer and large magnetization changes allows us to directly characterize the strong multiferroic coupling that can occur in flexible, nanostructured composites.

Evolutionary repair: Changes in multiple functional modules allow meiotic cohesin to support mitosis.

The role of proteins often changes during evolution, but we do not know how cells adapt when a protein is asked to participate in a different biological function. We forced the budding yeast, Saccharomyces cerevisiae, to use the meiosis-specific kleisin, recombination 8 (Rec8), during the mitotic cell cycle, instead of its paralog, Scc1. This perturbation impairs sister chromosome linkage, advances the timing of genome replication, and reduces reproductive fitness by 45%. We evolved 15 parallel populations for 1,750 generations, substantially increasing their fitness, and analyzed the genotypes and phenotypes of the evolved cells. Only one population contained a mutation in Rec8, but many populations had mutations in the transcriptional mediator complex, cohesin-related genes, and cell cycle regulators that induce S phase. These mutations improve sister chromosome cohesion and delay genome replication in Rec8-expressing cells. We conclude that changes in known and novel partners allow cells to use an existing protein to participate in new biological functions.

Dollars and Sense: The Business of Pediatric Surgery.

INTRODUCTION: This study evaluated North American pediatric surgeons' opinions and knowledge of business and economics in medicine and their perceptions of trends in their healthcare delivery environment. METHODS: We conducted an elective online survey of 1119 American Pediatric Surgical Association members. Over 8 mo, we iteratively developed the survey focused on four areas: opinion, knowledge, current practice environment, and trends in practice environment over the past 5 y. RESULTS: We received 227 (20.3%) complete surveys from pediatric surgeons. One hundred ninety four (85.5%) perceive healthcare as a business and most (85.9%) believe healthcare decisions may affect patients' out-of-pocket expenses. More than half (51.1%) of surgeons believe it has become more challenging to perform emergent cases and most believe staff quality has decreased for elective (56.4%) and emergent (63.0%) cases over the past 5 y. CONCLUSIONS: Pediatric surgeons recognize that medicine is a business and have concerns regarding the decreasing quality of operating room staff and the increasing difficulty providing surgical care over the last 5 y.

A supernumerary synthetic chromosome in Komagataella phaffii as a repository for extraneous genetic material.

BACKGROUND: Komagataella phaffii (Pichia pastoris) is a methylotrophic commercially important non-conventional species of yeast that grows in a fermentor to exceptionally high densities on simple media and secretes recombinant proteins efficiently. Genetic engineering strategies are being explored in this organism to facilitate cost-effective biomanufacturing. Small, stable artificial chromosomes in K. phaffii could offer unique advantages by accommodating multiple integrations of extraneous genes and their promoters without accumulating perturbations of native chromosomes or exhausting the availability of selection markers. RESULTS: Here, we describe a linear "nano"chromosome (of 15-25 kb) that, according to whole-genome sequencing, persists in K. phaffii over many generations with a copy number per cell of one, provided non-homologous end joining is compromised (by KU70-knockout). The nanochromosome includes a copy of the centromere from K. phaffii chromosome 3, a K. phaffii-derived autonomously replicating sequence on either side of the centromere, and a pair of K. phaffii-like telomeres. It contains, within its q arm, a landing zone in which genes of interest alternate with long (approx. 1-kb) non-coding DNA chosen to facilitate homologous recombination and serve as spacers. The landing zone can be extended along the nanochromosome, in an inch-worming mode of sequential gene integrations, accompanied by recycling of just two antibiotic-resistance markers. The nanochromosome was used to express PDI, a gene encoding protein disulfide isomerase. Co-expression with PDI allowed the production, from a genomically integrated gene, of secreted murine complement factor H, a plasma protein containing 40 disulfide bonds. As further proof-of-principle, we co-expressed, from a nanochromosome, both PDI and a gene for GFP-tagged human complement factor H under the control of PAOX1 and demonstrated that the secreted protein was active as a regulator of the complement system. CONCLUSIONS: We have added K. phaffii to the list of organisms that can produce human proteins from genes carried on a stable, linear, artificial chromosome. We envisage using nanochromosomes as repositories for numerous extraneous genes, allowing intensive engineering of K. phaffii without compromising its genome or weakening the resulting strain.

Disparities in care of pediatric, adolescent, and young adult patients with solid tumors: A systematic review.

BACKGROUND: Numerous studies have demonstrated a variety of social inequalities within pediatric and young adult patients with solid tumors. This systematic review examines and consolidates the existing literature regarding disparities in pediatric and young adult solid tumor oncology. PROCEDURE: A MeSH search was performed on the following databases: MEDLINE, PubMed, OvidSP Cochrane, Central, Embase, Cinhal, and Scopus. The systematic review was performed using Rayyan QCRI. RESULTS: Total 387 articles were found on the initial search, and 34 articles were included in final review. Twenty-seven studies addressed racial and ethnic disparities; 23 addressed socioeconomic disparities. Patients with Hispanic ethnicity, Black race, and lower socioeconomic status were more likely to present at later stages, have differences in treatments and higher mortality rates. CONCLUSION: This qualitative systematic review identified both racial and socioeconomic disparities in pediatric cancer patients across a variety of solid tumor types. Patients with Hispanic ethnicity, Black race, and lower socioeconomic status are associated with disparities in stage at presentation, treatment, and outcome. Characterization of existing disparities provides the evidence necessary to support changes at a systemic level.

The influence of prolonged instrument manipulation on gas leakage through trocars.

BACKGROUND: During laparoscopic surgery, CO2 insufflation gas could leak from the intra-abdominal cavity into the operating theater. Medical staff could therefore be exposed to hazardous substances present in leaked gas. Although previous studies have shown that leakage through trocars is a contributing factor, trocar performance over longer periods remains unclear. This study investigates the influence of prolonged instrument manipulation on gas leakage through trocars. METHODS: Twenty-five trocars with diameters ranging from 10 to 15 mm were included in the study. An experimental model was developed to facilitate instrument manipulation in a trocar under loading. The trocar was mounted to a custom airtight container insufflated with CO2 to a pressure of 15 mmHg, similar to clinical practice. A linear stage was used for prolonged instrument manipulation. At the same time, a fixed load was applied radially to the trocar cannula to mimic the reaction force of the abdominal wall. Gas leakage was measured before, after, and during instrument manipulation. RESULTS: After instrument manipulation, leakage rates per trocar varied between 0.0 and 5.58 L/min. No large differences were found between leakage rates before and after prolonged manipulation in static and dynamic measurements. However, the prolonged instrument manipulation did cause visible damage to two trocars and revealed unintended leakage pathways in others that can be related to production flaws. CONCLUSION: Prolonged instrument manipulation did not increase gas leakage rates through trocars, despite damage to some individual trocars. Nevertheless, gas leakage through trocars occurs and is caused by different trocar-specific mechanisms and design issues.

Escape of surgical smoke particles, comparing conventional and valveless trocar systems.

BACKGROUND: During minimal access surgery, surgical smoke is produced which can potentially be inhaled by the surgical team, leading to several health risks. This smoke can escape from the abdominal cavity into the operating room due to trocar leakage. The trocars and insufflator that are used during surgery influence gas leakage. Therefore, this study compares particle escape from a valveless (Conmed AirSeal iFS), and a conventional (Karl Storz Endoflator) system. MATERIALS AND METHODS: Using an in vitro model, a conventional and a valveless trocar system were compared. A protocol that simulated various surgical phases was defined to assess the surgical conditions and particle leakage. Insufflation pressures and instrument diameters were varied as these are known to affect gas leakage. RESULTS: The conventional trocar leaked during two distinct phases. Removal of the obturator caused a sudden release of particles. During instrument insertion, an average of 211 (IQR 111) particles per second escaped when using the 5 mm diameter instrument. With the 10 mm instrument, 50 (IQR 13) particles per second were measured. With the conventional trocar, a higher abdominal pressure increased particle leakage. The valveless trocar demonstrated a continuously high particle release during all phases. After the obturator was removed, particle escape increased sharply. Particle escape decreased to 1276 (IQR 580) particles per second for the 5 mm instrument insertion, and 1084 (IQR 630) particles per second for 10 mm instrument insertion. With the valveless trocar system, a higher insufflation pressure lowered particle escape. CONCLUSIONS: This study shows that a valveless trocar system releases more particles into the operating room environment than a conventional trocar. During instrument insertion, the leakage through the valveless system is 6 to 20 times higher than the conventional system. With a valveless trocar, leakage decreases with increasing pressure. With both trocar types leakage depends on instrument diameter.

Predicting pharmacotherapeutic outcomes for type 2 diabetes: An evaluation of three approaches to leveraging electronic health record data from multiple sources.

Electronic health record (EHR) data are increasingly used to develop prediction models to support clinical care, including the care of patients with common chronic conditions. A key challenge for individual healthcare systems in developing such models is that they may not be able to achieve the desired degree of robustness using only their own data. A potential solution-combining data from multiple sources-faces barriers such as the need for data normalization and concerns about sharing patient information across institutions. To address these challenges, we evaluated three alternative approaches to using EHR data from multiple healthcare systems in predicting the outcome of pharmacotherapy for type 2 diabetes mellitus(T2DM). Two of the three approaches, named Selecting Better (SB) and Weighted Average(WA), allowed the data to remain within institutional boundaries by using pre-built prediction models; the third, named Combining Data (CD), aggregated raw patient data into a single dataset. The prediction performance and prediction coverage of the resulting models were compared to single-institution models to help judge the relative value of adding external data and to determine the best method to generate optimal models for clinical decision support. The results showed that models using WA and CD achieved higher prediction performance than single-institution models for common treatment patterns. CD outperformed the other two approaches in prediction coverage, which we defined as the number of treatment patterns predicted with an Area Under Curve of 0.70 or more. We concluded that 1) WA is an effective option for improving prediction performance for common treatment patterns when data cannot be shared across institutional boundaries and 2) CD is the most effective approach when such sharing is possible, especially for increasing the range of treatment patterns that can be predicted to support clinical decision making.

Characterisation of trocar associated gas leaks during laparoscopic surgery.

BACKGROUND: During laparoscopy, the abdominal cavity is insufflated with carbon dioxide (CO2) that could become contaminated with viruses and surgical smoke. Medical staff is potentially exposed when this gas leaks into the operating room through the instruments and past trocar valves. No detailed studies currently exist that have quantified these leakage pathways. Therefore, the goal of this study was to quantify the gas leakages through trocars and instruments, during minimally invasive procedures. METHODS: A model of the surgical environment was created, consisting of a rigid container with an interface for airtight clamping of laparoscopic equipment such as trocars and surgical instruments. The model was insufflated to 15 mm Hg using a pressure generator and a pneumotachograph measured the equipment gas leak. A protocol of several use cases was designed to simulate the motions and forces the surgeon exerts on the trocar during surgery. RESULTS: Twenty-three individual trocars and twenty-six laparoscopic instruments were measured for leakage under the different conditions of the protocol. Trocar leakages varied between 0 L/min and more than 30 L/min, the instruments revealed a range of leakages between 0 L/min and 5.5 L/min. The results showed that leakage performance varied widely between trocars and instruments and that the performance and location of the valves influenced trocar leakage. CONCLUSIONS: We propose trocar redesigns to overcome specific causes of gas leaks. Moreover, an international testing standard for CO2 leakage for all new trocars and instruments is needed so surgical teams can avoid this potential health hazard when selecting new equipment.

Genetic Architecture of Maize Rind Strength Revealed by the Analysis of Divergently Selected Populations.

The strength of the stalk rind, measured as rind penetrometer resistance (RPR), is an important contributor to stalk lodging resistance. To enhance the genetic architecture of RPR, we combined selection mapping on populations developed by 15 cycles of divergent selection for high and low RPR with time-course transcriptomic and metabolic analyses of the stalks. Divergent selection significantly altered allele frequencies of 3,656 and 3,412 single- nucleotide polymorphisms (SNPs) in the high and low RPR populations, respectively. Surprisingly, only 110 (1.56%) SNPs under selection were common in both populations, while the majority (98.4%) were unique to each population. This result indicated that high and low RPR phenotypes are produced by biologically distinct mechanisms. Remarkably, regions harboring lignin and polysaccharide genes were preferentially selected in high and low RPR populations, respectively. The preferential selection was manifested as higher lignification and increased saccharification of the high and low RPR stalks, respectively. The evolution of distinct gene classes according to the direction of selection was unexpected in the context of parallel evolution and demonstrated that selection for a trait, albeit in different directions, does not necessarily act on the same genes. Tricin, a grass-specific monolignol that initiates the incorporation of lignin in the cell walls, emerged as a key determinant of RPR. Integration of selection mapping and transcriptomic analyses with published genetic studies of RPR identified several candidate genes including ZmMYB31, ZmNAC25, ZmMADS1, ZmEXPA2, ZmIAA41 and hk5. These findings provide a foundation for an enhanced understanding of RPR and the improvement of stalk lodging resistance.

A method for quantitative evaluations of scanning-proton dose distributions.

PURPOSE: Patient-Specific Quality Assurance (PSQA) measurement analysis depends on generating metrics representative of calculation and measurement agreement. Considering the heightened capability of discrete spot scanning protons to modulate individual dose voxels, a dose plane comparison approach that maintained all of the capabilities of the well-established γ test, but that also provided a more intuitive error parameterization, was desired. METHODS: Analysis was performed for 300 dose planes compared by searching all calculated points within a fixed radius around each measured pixel to determine the dose deviation. Dose plane agreement is reported as the dose difference minimum (DDM) within an empirically established search radius: ΔDmin(r). This per-pixel metric is aggregated into a histogram binned by dose deviation. Search-radius criteria were based on a weighted-beamlet 3σ spatial deviation from imaging isocenter. Equipment setup error was mitigated during analysis using tracked image registration, ensuring beamlet deviations to be the dominant source of spatial error. The percentage of comparison points with <3% dose difference determined pass rate. RESULTS: The mean beamlet radial deviation was 0.38mm from x-ray isocenter, with a standard deviation of 0.19mm, such that 99.9% of relevant pencil beams were within 1 mm of nominal. The dose-plane comparison data showed no change in passing rate between a 3%/1mm ΔDmin(r) analysis (97.6 +/- 3.6%) and a 3%/2mm γ test (97.7 +/- 3.2%). CONCLUSIONS: PSQA dose-comparison agreements corresponding to a search radius outside of machine performance limits are likely false positives. However, the elliptical shape of the γ test is too dose-restrictive with a spatial-error threshold set at 1 mm. This work introduces a cylindrical search shape, proposed herein as more relevant to plan quality, as part of the new DDM planar-dose comparison algorithm. DDM accepts all pixels within a given dose threshold inside the search radius, and carries forward plan-quality metrics in a straightforward manner for evaluation.

Irradiation-induced reactions at the CeO2/SiO2/Si interface.

The influence of high-energy (1.6 MeV) Ar2+ irradiation on the interfacial interaction between cerium oxide thin films (∼15 nm) with a SiO2/Si substrate is investigated using transmission electron microscopy, ultrahigh vacuum x-ray photoelectron spectroscopy (XPS), and a carbon monoxide (CO) oxidation catalytic reaction using ambient pressure XPS. The combination of these methods allows probing the dynamics of vacancy generation and its relation to chemical interactions at the CeO2/SiO2/Si interface. The results suggest that irradiation causes amorphization of some portion of CeO2 at the CeO2/SiO2/Si interface and creates oxygen vacancies due to the formation of Ce2O3 at room temperature. The subsequent ultra-high-vacuum annealing of irradiated films increases the concentration of Ce2O3 with the simultaneous growth of the SiO2 layer. Interactions with CO molecules result in an additional reduction of cerium and promote the transition of Ce2O3 to a silicate compound. Thermal annealing of thin films exposed to oxygen or carbon monoxide shows that the silicate phase is highly stabile even at 450 °C.

Biochemistry of N-mustard tumour control compounds reconsidered.

The biochemicals and reactions involved in the present mechanism of degradation of tumour cells during chemotherapy are reconsidered and limitations noted. Alternative mechanisms and treatment methods are detailed.

Preventing lodging in bioenergy crops: a biomechanical analysis of maize stalks suggests a new approach.

The hypothetical ideal for maize (Zea mays) bioenergy production would be a no-waste plant: high-yielding, with silage that is easily digestible for conversion to biofuel. However, increased digestibility is typically associated with low structural strength and a propensity for lodging. The solution to this dilemma may lie in our ability to optimize maize morphology using tools from structural engineering. To investigate how material (tissue) and geometric (morphological) factors influence stalk strength, detailed structural models of the maize stalk were created using finite-element software. Model geometry was obtained from high-resolution x-ray computed tomography (CT) scans, and scan intensity information was integrated into the models to infer inhomogeneous material properties. A sensitivity analysis was performed by systematically varying material properties over broad ranges, and by modifying stalk geometry. Computational models exhibited realistic stress and deformation patterns. In agreement with natural failure patterns, maximum stresses were predicted near the node. Maximum stresses were observed to be much more sensitive to changes in dimensions of the stalk cross section than they were to changes in material properties of stalk components. The average sensitivity to geometry was found to be more than 10-fold higher than the average sensitivity to material properties. These results suggest a new strategy for the breeding and development of bioenergy maize varieties in which tissue weaknesses are counterbalanced by relatively small increases (e.g. 5%) in stalk diameter that reduce structural stresses.

On measuring the bending strength of septate grass stems.

UNLABELLED: • PREMISE OF THE STUDY: Reliable testing methodologies are a fundamental tenet of scientific research. However, very little information is found in the literature explaining how to accurately measure the structural bending strength of plant stems. It was hypothesized that the most commonly employed loading configuration used in bending experiments (placement of loading anvil at an internodal region of the stem or stalk) may significantly alter test results and introduce errors in bending strength measurements of plant stems.• METHODS: Four types of mechanical tests were performed on bamboo (Phyllostachys aurea), giant reed (Arundo donax), and maize (Zea mays) to investigate how different loading configurations employed during three-point bending experiments affect test results of septate grass stems and to develop a testing protocol that provides reliable measures of stalk bending strength.• RESULTS: RESULTS confirmed the hypothesis that internodal-loaded three-point bending test can produce erroneous bending strength measurements. This testing methodology causes plant stems to break prematurely and produces failure types and patterns incongruent with stalks that broke in their natural (in situ) environment. In contrast, a modified test configuration produces natural failure patterns and more accurate measurements of bending strength.• CONCLUSION: Reliable measurements of stalk bending strength can be obtained by maximizing the span length of bending tests and placing the loading anvil at stronger and denser nodal tissues. These results are relevant to ecological and evolutionary plant biomechanics studies as well as agronomic breeding studies focused on measuring plant phenotypes such as stalk lodging strength, or on improving bending strength of septate plant stems.