bluuebunny/crossref_metadata_2025 huggingface dataset:
CRISPR/Cas9-mediated genome editing reveals 30 testis-enriched genes dispensable for male fertility in mice†
Authors: Lu Yonggang , Oura Seiya , Matsumura Takafumi , Oji Asami , Sakurai Nobuyuki , Fujihara Yoshitaka , Shimada Keisuke , Miyata Haruhiko , Tobita Tomohiro , Noda Taichi , Castaneda Julio M , Kiyozumi Daiji , Zhang Qian , Larasati Tamara , Young Samantha A M , Kodani Mayo , Huddleston Caitlin A , Robertson Matthew J , Coarfa Cristian , Isotani Ayako , Aitken R John , Okabe Masaru , Matzuk Martin M , Garcia Thomas X , Ikawa Masahito
Published: June 2019

More than 1000 genes are predicted to be predominantly expressed in mouse testis, yet many of them remain unstudied in terms of their roles in spermatogenesis and sperm function and their essentiality in male reproduction. Since individually indispensable factors can provide important implications for the diagnosis of genetically related idiopathic male infertility and may serve as candidate targets for the development of nonhormonal male contraceptives, our laboratories continuously analyze the functions of testis-enriched genes in vivo by generating knockout mouse lines using the CRISPR/Cas9 system. The dispensability of genes in male reproduction is easily determined by examining the fecundity of knockout males. During our large-scale screening of essential factors, we knocked out 30 genes that have a strong bias of expression in the testis and are mostly conserved in mammalian species including human. Fertility tests reveal that the mutant males exhibited normal fecundity, suggesting these genes are individually dispensable for male reproduction. Since such functionally redundant genes are of diminished biological and clinical significance, we believe that it is crucial to disseminate this list of genes, along with their phenotypic information, to the scientific community to avoid unnecessary expenditure of time and research funds and duplication of efforts by other laboratories.
SNAP23 is required for constitutive and regulated exocytosis in mouse oocytes†
Authors: Mehlmann Lisa M , Uliasz Tracy F , Lowther Katie M
Published: June 2019

Mammalian oocytes are stored in the ovary for prolonged periods, and arrested in meiotic prophase. During this period, their plasma membranes are constantly being recycled by endocytosis and exocytosis. However, the function of this membrane turnover is unknown. Here, we investigated the requirement for exocytosis in the maintenance of meiotic arrest. Using Trim-away, a newly developed method for rapidly and specifically depleting proteins in oocytes, we have identified the SNARE protein, SNAP23, to be required for meiotic arrest. Degradation of SNAP23 causes premature meiotic resumption in follicle-enclosed oocytes. The reduction in SNAP23 is associated with loss of gap junction communication between the oocyte and surrounding follicle cells. Reduction of SNAP23 protein also inhibits regulated exocytosis in response to a Ca2+ stimulus (cortical granule exocytosis), as measured by lectin staining and cleavage of ZP2. Our results show an essential role for SNAP23 in two key processes that occur in mouse oocytes and eggs.
Recruitment of monocytes and mature macrophages in mouse pubic symphysis relaxation during pregnancy and postpartum recovery†
Authors: Castelucci Bianca G , Consonni Silvio R , Rosa Viviane S , Joazeiro Paulo P
Published: June 2019

Appropriate remodeling of the female lower reproductive tract and pelvic floor is essential during normal mammalian pregnancy, labor, and postpartum recovery. During mouse pregnancy, in addition to reproductive tract modifications, the pubic symphysis (PS) is remodeled into a soft interpubic ligament (IpL) to provide safe delivery of the offspring and fast postpartum recovery. Although temporal changes in the phenotypes of myeloid cells, such as mononuclear phagocytes, are crucial to remodeling the lower reproductive tract organs in preparation for a safe delivery, little is known about the involvement of recruited monocytes or macrophages in mouse PS remodeling. We used combined light microscopy, electron microscopy, and qPCR analysis to investigate the profile of recruited monocytes and macrophage polarization markers in C57Bl6 mouse interpubic tissues during pregnancy (D12, D18, and D19) and early days postpartum (1 dpp and 3 dpp) to better identify their presence in proper remodeling of the mouse PS. Our morphological data show that the number of recruited monocytes is increased in interpubic tissues and that recruited monocytes differentiate into proinflammatory or anti-inflammatory macrophage phenotypes from D18 to 3 dpp, which may contribute to dynamic changes in the gene expression of specific inflammatory mediators involved in interpubic tissue remodeling at these time points. Therefore, our morphological and quantitative gene expression data suggest that both differentiated macrophages from recruited monocytes and polarized macrophages may collaborate for IpL relaxation at labor and the appropriate repair of the PS after the first pregnancy.
Nanopore Sequencing Significantly Improves Genome Assembly of the Protozoan Parasite Trypanosoma cruzi
Authors: Díaz-Viraqué Florencia , Pita Sebastián , Greif Gonzalo , de Souza Rita de Cássia Moreira , Iraola Gregorio , Robello Carlos
Published: June 2019

Chagas disease was described by Carlos Chagas, who first identified the parasite Trypanosoma cruzi from a 2-year-old girl called Berenice. Many T. cruzi sequencing projects based on short reads have demonstrated that genome assembly and downstream comparative analyses are extremely challenging in this species, given that half of its genome is composed of repetitive sequences. Here, we report de novo assemblies, annotation, and comparative analyses of the Berenice strain using a combination of Illumina short reads and MinION long reads. Our work demonstrates that Nanopore sequencing improves T. cruzi assembly contiguity and increases the assembly size in ∼16 Mb. Specifically, we found that assembly improvement also refines the completeness of coding regions for both single-copy genes and repetitive transposable elements. Beyond its historical and epidemiological importance, Berenice constitutes a fundamental resource because it now constitutes a high-quality assembly available for TcII (clade C), a prevalent lineage causing human infections in South America. The availability of Berenice genome expands the known genetic diversity of these parasites and reinforces the idea that T. cruzi is intraspecifically divided in three main clades. Finally, this work represents the introduction of Nanopore technology to resolve complex protozoan genomes, supporting its subsequent application for improving trypanosomatid and other highly repetitive genomes.
The Effects of Metformin on Age-Related Changes in the Liver Sinusoidal Endothelial Cell
Authors: Hunt Nicholas J , Lockwood Glen P , Kang Sun Woo (Sophie) , Pulpitel Tamara , Clark Ximonie , Mao Hong , McCourt Peter A G , Cooney Gregory J , Wali Jibran A , Le Couteur Frank H , Le Couteur David G , Cogger Victoria C
Published: June 2019

Age-related changes in the liver sinusoidal endothelium, particularly the reduction in fenestrations, contribute to insulin resistance in old age. Metformin impacts on the aging process and improves insulin resistance. Therefore, the effects of metformin on the liver sinusoidal endothelium were studied. Metformin increased fenestrations in liver sinusoidal endothelial cells isolated from both young and old mice. Mice administered metformin in the diet for 12 months had increased fenestrations and this was associated with lower insulin levels. The effect of metformin on fenestrations was blocked by inhibitors of AMP-activated protein kinase (AMPK), endothelial nitric oxide synthase, and myosin light chain kinase phosphorylation. Metformin led to increased transgelin expression and structural changes in the actin cytoskeleton but had no effect on lactate production. Metformin also generated fenestration-like structures in SK-Hep1 cells, a liver endothelial cell line, and this was associated with increased ATP, cGMP, and mitochondrial activity. In conclusion, metformin ameliorates age-related changes in the liver sinusoidal endothelial cell via AMPK and endothelial nitric oxide pathways, which might promote insulin sensitivity in the liver, particularly in old age.
Decellularized Human Gut as a Natural 3D Platform for Research in Intestinal Fibrosis
Authors: Giuffrida Paolo , Curti Marco , Al-Akkad Walid , Biel Carin , Crowley Claire , Frenguelli Luca , Telese Andrea , Hall Andrew , Tamburrino Domenico , Spoletini Gabriele , Fusai Giuseppe , Tinozzi Francesco Paolo , Pietrabissa Andrea , Corazza Gino Roberto , De Coppi Paolo , Pinzani Massimo , Di Sabatino Antonio , Rombouts Krista , Mazza Giuseppe
Published: June 2019

Background

The current methodologies for the identification of therapeutic targets for inflammatory bowel disease (IBD) are limited to conventional 2-dimensional (2D) cell cultures and animal models. The use of 3D decellularized human intestinal scaffolds obtained from surgically resected intestine and engineered with human intestinal cells may provide a major advancement in the development of innovative intestinal disease models. The aim of the present study was to design and validate a decellularization protocol for the production of acellular 3D extracellular matrix (ECM) scaffolds from the human duodenum.

Methods

Scaffolds were characterized by verifying the preservation of the ECM protein composition and 3D architecture of the native intestine and were employed for tissue engineering with primary human intestinal myofibroblasts for up to 14 days.

Results

Engrafted cells showed the ability to grow and remodel the surrounding ECM. mRNA expression of key genes involved in ECM turnover was significantly different when comparing primary human intestinal myofibroblasts cultured in 3D scaffolds with those cultured in standard 2D cultures on plastic dishes. Moreover, incubation with key profibrogenic growth factors such as TGFβ1 and PDGF-BB resulted in markedly different effects in standard 2D vs 3D cultures, further emphasizing the importance of using 3D cell cultures.

Conclusions

These results confirm the feasibility of 3D culture of human intestinal myofibroblasts in intestinal ECM scaffolds as an innovative platform for disease modeling, biomarker discovery, and drug testing in intestinal fibrosis.
Su salud a la mano (your health at hand): patient perceptions about a bilingual patient portal in the Los Angeles safety net
Authors: Casillas Alejandra , Perez-Aguilar Giselle , Abhat Anshu , Gutierrez Griselda , Olmos-Ochoa Tanya T , Mendez Carmen , Mahajan Anish , Brown Arleen , Moreno Gerardo
Published: June 2019

Objectives

Driven by beneficial patient-centered outcomes associated with patient portal use and the Affordable Care Act, portal implementation has expanded into safety nets—health systems that offer access to care to a large share of uninsured, Medicaid, and other vulnerable populations. However, little attention has been paid to the factors that affect portal accessibility by the vulnerable patients served by these health systems—including those who are limited English proficient (LEP).

Materials and Methods

The Los Angeles County Department of Health Services (LAC DHS), the second-largest safety net system in the nation, launched its first patient portal, and one of the few bilingual English-Spanish interfaces in existence, in March of 2015. To explore portal awareness and perceptions, we conducted focus groups with LAC DHS patients, in English and Spanish (LEP). The Technology Acceptance Model was used to guide thematic analysis of focus group data.

Results

Of the 46 participants, 37 were patients and 9 were caretakers; 23 were English-speaking and 23 Spanish-speaking LEP. All patients had diabetes or hypertension. Over half had an annual household income <$10 000, yet 78% of English-speaking and 65% of Spanish-speaking LEP participants reported at-home Internet access. Participants’ discussion centered around 3 major thematic narratives: (1) participants’ awareness or attitudes about the LAC DHS portal; (2) role of culture, language, or community with regard to portal accessibility and utility; and (3) perceived needs for successful portal implementation.

Conclusions

Safety net participants identified concrete benefits to the portal and emphasized the need for portal engagement that offered accessible education, support, and resources in clinical and community settings. The portal offers an additional opportunity to engage the patient and family with trusted and validated health information, and should be further developed in this capacity. This study provides a better understanding of preferred improvements of patient portal engagement that guide broader health technology efforts to address electronic health disparities.
The Bacteriological Profile of Burn Wound Infections at a Tertiary Burns Center in Nepal
Authors: Pujji Ojas Jyoti Singh , Nakarmi Kiran Kishor , Shrestha Basudha , Rai Shankar Man , Jeffery Steven Leonard Alexander
Published: June 2019

In Nepal, burn is the third most common injury after falls and road traffic accidents. Infection is the leading cause of mortality in burn injury. A profile exploring predominant flora and antimicrobial sensitivity is important to facilitate treatment ahead of microbiology results and to aid prevention of multidrug-resistant organisms. The aim of this study was to document epidemiological and bacteriological data of burn wound infections at a tertiary level burns center in Nepal. Samples were collected from January 2017 to May 2017, over a period of 5 months. Patient notes were referred to and information regarding baseline characteristics and burn wound infection data was collected. A total of 76 patients were included in the study during the 5-month period, which resulted in 113 samples being included for review. Females were injured most with burns 70% (n = 53) compared with males 30% (n = 23). Only 6 (8%) of 77 patients lived locally in Kathmandu. The average distance traveled by patients was 233 km (median 208, range 0–765, SD 181). Average TBSA% of burn was 22% (median 20, range 3–50, SD 12). Gram-negative organisms predominated, with Acinetobacter spp. in 42 cases (55%), Pseudomonas aeruginosa in 26 cases (34%), and Enterobacter spp. in 16 cases (21%). Colistin, polymyxin B, and tigecycline were found to be most sensitive covering 108, 98, and 94 organisms. Gram-negative bacteria colonized the majority of burn wounds. Colistin, polymyxin B, and tigecycline were the most sensitive to gram-negative bacteria. Gram-positive Staphylococcus aureus was sensitive most to vancomycin and tigecycline.
The Political Economy of Public Debt: A Laboratory Study
Authors: Battaglini Marco , Nunnari Salvatore , Palfrey Thomas R
Published: June 2019

This paper reports the results from a laboratory experiment designed to study political distortions in the accumulation of public debt. A legislature bargains over the levels of a public good and of district specific transfers in two periods. The legislature can issue or purchase risk-free bonds in the first period and the level of public debt creates a dynamic linkage across policymaking periods. In line with the theoretical predictions, we find that public policies are inefficient and efficiency is increasing in the size of the majority requirement, with higher investment in public goods and lower debt associated with larger majority requirements. Debt is lower when the probability of a negative shock to the economy in the second period is higher indicating that even in a political equilibrium debt is used to smooth consumption and to insure against economic uncertainty. Also in line with the theoretical predictions, we find that dynamic distortions are eliminated when the first period proposer can commit to a policy for both periods. The experiment, however, highlights two phenomena that are surprising in terms of standard theory and have not been previously documented. First, balancing the budget in each period is a focal point, leading to lower distortions than predicted. Second, higher majority requirements induce significant delays in reaching an agreement.
Effect of Fluctuating High Temperatures on House Flies (Diptera: Muscidae) and Their Principal Parasitoids (Muscidifurax spp. and Spalangia spp. [Hymenoptera: Pteromalidae]) From the United States
Authors: Geden Christopher J , Biale Haim , Chiel Elad , Johnson Dana M
Published: June 2019

Colonies of house flies (Musca domestica L. [Diptera: Muscidae]) and four species of parasitoids (Muscidifurax raptor Girault and Sanders, Muscidifurax zaraptor Kogan and Legner, Spalangia cameroni Perkins and Spalangia endius Walker) were established by making collections from dairy farms near Bell, FL, Beatrice, NE, Minneapolis, MN, and San Jacinto, CA. Colonies were assessed for heat tolerance by comparing life history parameters at 25–27°C and fluctuating hot (26.7–41.7°C) temperatures. Muscidifurax raptor, S. cameroni, and S. endius produced 24–28% as many progeny under hot conditions as at 25°C. Colonies of M. zaraptor were more heat-tolerant and produced an average 46.9% as many progeny under the hot regime compared with moderate conditions. There was little evidence for higher heat tolerance in parasitoid populations from historically hot locations (CA desert and FL). Colonies of M. raptor and S. endius that had been in culture for 24 yr were the least heat-tolerant with regard to progeny production. House flies collected from the same locations varied little in longevity, fecundity, or egg-to-adult survival under either hot or moderate regimes. Flies reared under hot conditions laid about half as many eggs (89/female) and had about half the egg–adult survival rate (47.3%) under hot compared with moderate conditions, indicating that heat stress had less effect on flies than on all of the parasitoids except M. zaraptor. An attempt to select for heat tolerance in flies by subjecting them to incremental increases in rearing temperatures for 20 generations resulted in little change in tolerance among the selected flies.
The effects of dynamical substructure on Milky Way mass estimates from the high-velocity tail of the local stellar halo
Authors: Grand Robert J J , Deason Alis J , White Simon D M , Simpson Christine M , Gómez Facundo A , Marinacci Federico , Pakmor Rüdiger
Published: June 2019

We investigate the impact of dynamical streams and substructure on estimates of the local escape speed and total mass of Milky-Way-mass galaxies from modelling the high-velocity tail of local halo stars. We use a suite of high-resolution magnetohydrodynamical cosmological zoom-in simulations that resolve phase space substructure in local volumes around solar-like positions. We show that phase space structure varies significantly between positions in individual galaxies and across the suite. Substructure populates the high-velocity tail unevenly and leads to discrepancies in the mass estimates. We show that a combination of streams, sample noise, and truncation of the high-velocity tail below the escape speed leads to a distribution of mass estimates with a median that falls below the true value by ${\sim } 20 {{\ \rm per\ cent}}$, and a spread of a factor of 2 across the suite. Correcting for these biases, we derive a revised value for the Milky Way mass presented in Deason et al. of $1.29 ^{+0.37}_{-0.47} \times 10^{12}\, \rm M_{\odot }$.
Fundamentals of Clinical Prediction Modeling for the Neurosurgeon
Authors: Mijderwijk Hendrik-Jan , Steyerberg Ewout W , Steiger Hans-Jakob , Fischer Igor , Kamp Marcel A
Published: June 2019

Clinical prediction models in neurosurgery are increasingly reported. These models aim to provide an evidence-based approach to the estimation of the probability of a neurosurgical outcome by combining 2 or more prognostic variables. Model development and model reporting are often suboptimal. A basic understanding of the methodology of clinical prediction modeling is needed when interpreting these models. We address basic statistical background, 7 modeling steps, and requirements of these models such that they may fulfill their potential for major impact for our daily clinical practice and for future scientific work.
Behavioral and Subjective Effects of Reducing Nicotine in Cigarettes: A Cessation Commentary
Authors: Piper Megan E , Drobes David J , Walker Natalie
Published: June 2019

This commentary addresses critical questions regarding the impact of the reduction of nicotine on changes in smoking behavior. There appears to be moderate evidence that use of reduced nicotine cigarettes (RNC) increases the likelihood of making a quit attempt among smokers unmotivated to quit and among smokers motivated to quit who also used nicotine replacement therapy (NRT). There was limited evidence that RNC combined with NRT increased smoking abstinence, regardless of motivation to quit. Several plausible mechanisms via which RNC may influence smoking behavior, including reducing dependence, are reviewed. The moderate evidence that abrupt reduction in nicotine reduces self-reported dependence as well as smoking behavior and likelihood of relapse is also reviewed. The data reviewed here suggest that abrupt switching to, and extended use of, RNC can reduce cigarette dependence and several related constructs, including the ability to quit smoking. The data reviewed in this commentary suggest that abrupt reduction in the level of nicotine in combustible cigarettes could reduce smoking behavior, nicotine dependence, and other related constructs and increase quit attempts and eventual smoking cessation.
A comparison between Zooglider and shipboard net and acoustic mesozooplankton sensing systems
Authors: Whitmore Benjamin M , Nickels Catherine F , Ohman Mark D
Published: June 2019

Some planktonic patches have markedly higher concentrations of organisms compared to ambient conditions and are <5 m in thickness (i.e. thin layers). Conventional net sampling techniques are unable to resolve this vertical microstructure, while optical imaging systems can measure it for limited durations. Zooglider, an autonomous zooplankton-sensing glider, uses a low-power optical imaging system (Zoocam) to resolve mesozooplankton at a vertical scale of 5 cm while making concurrent physical and acoustic measurements (Zonar). In March 2017, Zooglider was compared with traditional nets (MOCNESS) and ship-based acoustics (Simrad EK80). Zoocam recorded significantly higher vertically integrated abundances of smaller copepods and appendicularians, and larger gelatinous predators and mineralized protists, but similar abundances of chaetognaths, euphausiids, and nauplii. Differences in concentrations and size-frequency distributions are attributable to net extrusion and preservation artifacts, suggesting advantages of in situ imaging of organisms by Zooglider. Zoocam detected much higher local concentrations of copepods and appendicularians (53 000 and 29 000 animals m−3, respectively) than were resolvable by nets. The EK80 and Zonar at 200 kHz agreed in relative magnitude and distribution of acoustic backscatter. The profiling capability of Zooglider allows for deeper high-frequency acoustic sampling than conventional ship-based acoustics.
IgG4-related disease in a multi-ethnic community: clinical characteristics and association with malignancy
Authors: Poo S X , Tham C S W , Smith C , Lee J , Cairns T , Galliford J , Hamdulay S , Jacyna M , Levy J B , McAdoo S P , Roufosse C , Wernig F , Mason J C , Pusey C D , Tam F W K , Tomlinson J A P
Published: June 2019

Background

Immunoglobulin-G4-related disease (IgG4-RD) is a recently recognized fibro-inflammatory condition that can affect multiple organs. Despite growing interest in this condition, the natural history and management of IgG4-RD remain poorly understood.

Aim

To describe the clinical characteristics, treatment and outcomes of IgG4-RD in a multi-ethnic UK cohort, and investigate its possible association with malignancy.

Design

Retrospective analysis of case-note and electronic data.

Methods

Cases were identified from sub-specialty cohorts and a systematic search of an NHS trust histopathology database using ‘IgG4’ or ‘inflammatory pseudotumour’ as search terms. Electronic records, imaging and histopathology reports were reviewed.

Results

In total, 66 identified cases of IgG4-RD showed a similar multi-ethnic spread to the local population of North West London. The median age was 59 years and 71% of patients were male. Presenting symptoms relating to mass effect of a lesion were present in 48% of cases and the mean number of organs involved was 2.4. Total of 10 patients had reported malignancies with 6 of these being haematological. 83% of those treated with steroids had good initial response; however, 50% had relapsing-remitting disease. Rituximab was administered in 11 cases and all achieved an initial serological response. Despite this, seven patients subsequently relapsed after a mean duration of 11 months and four progressed despite treatment.

Conclusions

We report a large UK-based cohort of IgG4-RD that shows no clear ethnic predisposition and a wide range of affected organs. We discuss the use of serum IgG4 concentrations as a disease marker in IgG4-RD, the association with malignant disease and outcomes according to differing treatment regimens.
The Decline of Intergenerational Income Mobility in Denmark: Returns to Education, Demographic Change, and Labor Market Experience☆
Authors: Harding David J , Munk Martin D
Published: June 2019

Although there is some evidence of declining intergenerational mobility in wealthy countries, the sources of these changes are not well understood. This paper examines the changes in intergenerational mobility in Denmark, which has one of the highest levels of intergenerational mobility in the world. We show that mobility has been declining for both men and women since the late 1950s across the most recent cohorts who are now old enough to measure permanent adult income, and that these changes were concentrated among children born into the middle three-fifths of the income distribution. We examine the sources of this decline by testing hypotheses related to demographic processes, returns to education, and work experience. Our results highlight the importance of both parent and child work experience and family structure in the family of origin among both men and women as well as, to a lesser degree, marital status, assortative mating, and childbearing among women. Although education was an important driver of parent-child income rank associations (IRA) in each cohort, it played little role in accounting for increases in those associations across cohorts.
Determination of true patient origin through motorcycle mapping: design and implementation of a community-defined geographic infrastructure surveillance tool in rural Sierra Leone
Authors: Monk Edward J M , Yee Ka-Ping , Allan Rupert , Gayton Ivan B
Published: June 2019

Background

Village-level geographic infrastructure data are often insufficient in low-resource settings, despite accurate patient origin determination being essential for surveillance and outbreak management. We detail a novel and seemingly reliable method for the determination of true patient origin with proof of concept in rural Sierra Leone.

Methods

Potential villages (n=2263), identified within a 7800 km2 hospital catchment area from satellite imagery, were accessed by motorcycle and surveyed in person, capturing village name and community-defined section/chiefdom/district.

Results

A survey established 1740 inhabited villages and a village of origin determination tool (gazetteer) was produced. Recording the district/chiefdom/section/village at hospital registration allowed Global Positioning System patient origin determination in 2277/2344 (97.1%) attendances.

Conclusions

Our proof of concept reports a substantial and sustained record of true patient origin in a low-resource setting.
Analysis of
in vivo
uterine peristalsis in the non-pregnant female mouse
Authors: Zhang Ying , Qian Jingjing , Zaltzhendler Oren , Bshara Mustafa , Jaffa Ariel J. , Grisaru Dan , Duan Enkui , Elad David
Published: June 2019

Uterine peristalsis due to spontaneous contractions of the myometrial smooth muscles has important roles in pre-implantation processes of intra-uterine sperm transport to the fertilization site, and then embryo transport to the implantation sites. We developed a new objective methodology to study
in vivo
uterine peristalsis in female mice during the pro-oestrus phase. The acquisition procedure of the uterine organ is remote without interfering with the organ function. The uniqueness of the new approach is that video images of physiological pattern were converted using image processing and new algorithms to biological time-dependent signals that can be processed with existing algorithms for signal processing. Using this methodology we found that uterine peristalsis in the pro-oestrus mouse is in the range of 0.008–0.029 Hz, which is about one contraction per minute and with fairly symmetric contractions that occasionally propagate caudally. This rate of contractions is similar to that of human uterine peristalsis acquired
in vivo
, which is important information for a popular animal model.
Biomechanical analysis of intact versus ruptured Poly Implant Prothèse breast implants
Authors: Ramião N. G. , Martins P. S. , Barroso M. L. , Santos D. C. , Fernandes A. A.
Published: June 2019

Despite there being many studies that have evaluated breast implant rupture, there is no consensus about causes and incidence. Most studies lack a multifactorial analysis of what causes breast implants to rupture. To fill this gap, an experimental protocol was developed to compare ruptured and intact Poly Implant Prothèse (PIP) breast implants from the same woman. These conditions guarantee that the physical/biological variables are the same for each pair of ruptured and intact implants. A total of 1008 samples from 22 PIP explants (11 intact and 11 ruptured) and three control PIP implants were analysed. The mechanical properties (tensile strength) of the ruptured and intact implants were compared according to brand, lot, implantation time and demographic conditions. In general, statistically significant differences were found between the intact and ruptured PIP implants. Ruptured implants were thinner (0.73 ± 0.10 mm versus 0.91 ± 0.11 mm) and weaker (7.42 ± 2.65 MPa versus 9.59 ± 2.37 MPa) than intact implants. Intact and ruptured implants have shown distinct mechanical behaviours and variations in thickness. Our understanding is that these differences may be associated with the typical manufacturing process of breast implant shells. These results stress the importance of thorough control of the shell thickness. Given its relevance, shell thickness should be used as a quality control measure for homologation purposes. Thus, the homogeneity of the shell should be considered as a relevant parameter during the manufacturing process. This will translate into an improved quality of life for patients and will potentiate safer and longer lasting products.
Mesenchymal stem cell-based bioengineered constructs: foreign body response, cross-talk with macrophages and impact of biomaterial design strategies for pelvic floor disorders
Authors: Mukherjee Shayanti , Darzi Saeedeh , Paul Kallyanashis , Werkmeister Jerome A. , Gargett Caroline E.
Published: June 2019

An excessive foreign body response (FBR) has contributed to the adverse events associated with polypropylene mesh usage for augmenting pelvic organ prolapse surgery. Consequently, current biomaterial research considers the critical role of the FBR and now focuses on developing better biocompatible biomaterials rather than using inert implants to improve the clinical outcomes of their use. Tissue engineering approaches using mesenchymal stem cells (MSCs) have improved outcomes over traditional implants in other biological systems through their interaction with macrophages, the main cellular player in the FBR. The unique angiogenic, immunomodulatory and regenerative properties of MSCs have a direct impact on the FBR following biomaterial implantation. In this review, we focus on key aspects of the FBR to tissue-engineered MSC-based implants for supporting pelvic organs and beyond. We also discuss the immunomodulatory effects of the recently discovered endometrial MSCs on the macrophage response to new biomaterials designed for use in pelvic floor reconstructive surgery. We conclude with a focus on considerations in biomaterial design that take into account the FBR and will likely influence the development of the next generation of biomaterials for gynaecological applications.
Development of anatomically based customizable three-dimensional finite-element model of pelvic floor support system: POP-SIM1.0
Authors: Gordon Mark T. , DeLancey John O. L. , Renfroe Aaron , Battles Andrew , Chen Luyun
Published: June 2019

To develop an anatomically based customizable finite-element (FE) model of the pelvic floor support system to simulate pelvic organ prolapse (POP): POP-SIM1.0. This new simulation platform allows for the construction of an array of models that objectively represent the key anatomical and functional variation in women with and without prolapse to test pathomechanism hypotheses of the prolapse formation. POP-SIM1.0 consists of anatomically based FE models and a suite of Python-based tools developed to rapidly construct FE models by customizing the base model with desired structural parameters. Each model consists of anatomical structures from three support subsystems which can be customized based on magnetic resonance image measurements in women with and without prolapse. The customizable structural parameters include presence of levator ani (LA) avulsion, hiatus size, anterior vaginal wall dimension, attachment fascia length and apical location in addition to the tissue material properties and intra-abdominal pressure loading. After customization, the FE model was loaded with increasing intra-abdominal pressure (0–100 cmH
2
O) and solved using ABAQUS explicit solver. We were able to rapidly construct anatomically based FE models with specific structural geometry which reflects the morphology changes often observed in women with prolapse. At maximum loading, simulated structural deformations have similar anatomical characteristics to those observed during clinical exams and stress magnetic resonance images. Simulation results showed the presence of LA muscle avulsion negatively impacts the pelvic floor support. The normal model with intact muscle had the smallest exposed vaginal length of 11 mm, while the bilateral avulsion produced the largest exposed vaginal length at 24 mm. The unilateral avulsion model had an exposed vaginal length of 18 mm and also demonstrated a tipped perineal body similar to that seen in clinical observation. Increasing the hiatus size, vaginal wall length and fascia length also resulted in worse pelvic floor support, increasing the exposed vaginal length from 18 mm in the base model to 33 mm, 54 mm and 23.5 mm, respectively. The developed POP-SIM1.0 can simulate the anatomical structure changes often observed in women with prolapse. Preliminary results showed that the presence of LA avulsion, enlarged hiatus, longer vaginal wall and fascia length can result in larger prolapse at simulated maximum Valsalva.
Small-molecule control of super-Mendelian inheritance in gene drives
Authors: López Del Amo Víctor , Leger Brittany S. , Cox Kurt J. , Gill Shubhroz , Bishop Alena L. , Scanlon Garrett D. , Walker James A. , Gantz Valentino M. , Choudhary Amit
Published: June 2019

By surpassing the 50% inheritance limit of Mendel’s law of independent assortment, CRISPR-based gene drives have the potential to fight vector-borne diseases or suppress crop pests. However, contemporary gene drives could spread unchecked, posing safety concerns that limit their use in both laboratory and field settings. Current technologies also lack chemical control strategies, which could be applied in the field for dose, spatial and temporal control of gene drives. We describe in Drosophila the first gene-drive system controlled by an engineered Cas9 and a synthetic, orally-available small molecule.

Graphical Abstract
Comparative genomic analyses reveal diverse virulence factors and antimicrobial resistance mechanisms in clinical Elizabethkingia meningoseptica strains
Authors: Chen Shicheng , Soehnlen Marty , Blom Jochen , Terrapon Nicolas , Henrissat Bernard , Walker Edward D.
Published: June 2019

Three human clinical isolates of bacteria (designated strains Em1, Em2 and Em3) had high average nucleotide identity (ANI) to Elizabethkingia meningoseptica. Their genome sizes (3.89, 4.04 and 4.04 Mb) were comparable to those of other Elizabethkingia species and strains, and exhibited open pan-genome characteristics, with two strains being nearly identical and the third divergent. These strains were susceptible only to trimethoprim/sulfamethoxazole and ciprofloxacin amongst 16 antibiotics in minimum inhibitory tests. The resistome exhibited a high diversity of resistance genes, including 5 different lactamase- and 18 efflux protein-encoding genes. Forty-four genes encoding virulence factors were conserved among the strains. Sialic acid transporters and curli synthesis genes were well conserved in E. meningoseptica but absent in E. anophelis and E. miricola. E. meningoseptica carried several genes contributing to biofilm formation. 58 glycoside hydrolases (GH) and 25 putative polysaccharide utilization loci (PULs) were found. The strains carried numerous genes encoding two-component system proteins (56), transcription factor proteins (187~191), and DNA-binding proteins (6~7). Several prophages and CRISPR/Cas elements were uniquely present in the genomes.
In vivo screen identifies LXR agonism potentiates sorafenib killing of hepatocellular carcinoma
Authors: Preziosi Morgan E. , Zahm Adam M. , Vázquez-Salgado Alexandra M. , Ackerman Daniel , Gade Terence P. , Kaestner Klaus H. , Wangensteen Kirk J.
Published: June 2019

Existing drug therapies for hepatocellular carcinoma (HCC), including sorafenib, extend patient survival by only three months. We sought to identify novel druggable targets for use in combination with sorafenib to increase its efficacy. We implemented an in vivo genetic screening paradigm utilizing a library of 43 genes-of-interest expressed in the context of repopulation of the injured livers of Fumarylacetoacetate Hydrolase-deficient (Fah−/−) mice, which led to highly penetrant HCC. We then treated mice with vehicle or sorafenib to discover genetic determinants of sensitivity and resistance. Liver X Receptor alpha (LXRα) emerged as a potential target. To examine LXRα agonism in combination with sorafenib treatment, we added varying concentrations of sorafenib and LXRα agonist drugs to HCC cell lines. We performed transcriptomic analysis to elucidate the mechanisms of HCC death. Fah−/− mice injected with the screening library developed HCC tumor clones containing Myc cDNA plus various other cDNAs. Treatment with sorafenib resulted in sorafenib-resistant HCCs that were significantly depleted in Nr1h3 cDNA, encoding LXRα, suggesting that LXRα activation is incompatible with tumor growth in the presence of sorafenib treatment in vivo. The combination of sorafenib and LXR agonism led to enhanced cell death as compared to monotherapy in multiple HCC cell lines, due to reduced expression of cell cycle regulators and increased expression of genes associated with apoptosis. Combination therapy also enhanced cell death in a sorafenib-resistant primary human HCC cell line. Our novel in vivo screen led to the discovery that LXR agonist drugs potentiate the efficacy of sorafenib in treating HCC.
The glucocorticoid receptor in the nucleus accumbens plays a crucial role in social rank attainment in rodents
Authors: Papilloud Aurélie , Weger Meltem , Bacq Alexandre , Zalachoras Ioannis , Hollis Fiona , Larrieu Thomas , Battivelli Dorian , Grosse Jocelyn , Zanoletti Olivia , Parnaudeau Sébastien , Tronche François , Sandi Carmen
Published: June 2019

Social hierarchy in social species is usually established through competitive encounters with conspecifics. It determines the access to limited resources and, thus, leads to reduced fights among individuals within a group. Despite the known importance of social rank for health and well-being, the knowledge about the processes underlying rank attainment remains limited. Previous studies have highlighted the nucleus accumbens (NAc) as a key brain region in the attainment of social hierarchies in rodents. In addition, glucocorticoids and the glucocorticoid receptor (GR) have been implicated in the establishment of social hierarchies and social aversion. However, whether GR in the NAc is involved in social dominance is not yet known. To address this question, we first established that expression levels of GR in the NAc of high anxious, submissive-prone rats are lower than that of their low anxious, dominant-prone counterparts. Furthermore, virally-induced downregulation of GR expression in the NAc in rats led to an improvement of social dominance rank. We found a similar result in a cell-specific mouse model lacking GR in dopaminoceptive neurons (i.e., neurons containing dopamine receptors). Indeed, when cohabitating in dyads of mixed genotypes, mice deficient for GR in dopaminoceptive neurons had a higher probability to become dominant than wild-type mice. Overall, our results highlight GR in the NAc and in dopaminoceptive neurons as an important regulator of social rank attainment.
BTLA and PD-1 employ distinct phosphatases to differentially repress T cell signaling
Authors: Xu Xiaozheng , Fulzele Amitkumar , Zhao Yunlong , Wu Zijun , Hu Yanyan , Jiang Yong , Ma Yanzhe , Wang Haopeng , Fu Guo , Bennett Eric , Hui Enfu
Published: June 2019

T cell-mediated destruction of tumors and virus-infected cells is restricted by co-inhibitory receptors such as programmed cell death protein 1 (PD-1). Monoclonal antibodies blocking PD-1 have produced impressive clinical activity against human cancers, but durable response is limited to a minority of patients. Previous results suggest that B and T lymphocyte attenuator (BTLA), a co-inhibitory receptor structurally related to PD-1, may contribute to the resistance to PD-1 targeted therapy and co-blockade of BTLA can enhance the efficacy of anti-PD-1 immunotherapy. However, the biochemical mechanism by which BTLA represses T cell activity and to what extent the mechanism differs from that of PD-1 is unknown. Here we examine differences in the ability of BTLA and PD-1 to recruit effector molecules and regulate T cell signaling. We show that PD-1 and BTLA recruit different tyrosine phosphatases to regulate either CD28 or T cell antigen receptor (TCR)-signaling cascades. Our data reveal unexpected disparities between two structurally related immune checkpoints and two phosphatase paralogs.
Machine learning identifies large-scale reward-related activity modulated by dopaminergic enhancement in major depression
Authors: Liu Yuelu , Admon Roee , Belleau Emily L. , Kaiser Roselinde H. , Clegg Rachel , Beltzer Miranda , Goer Franziska , Vitaliano Gordana , Ahammad Parvez , Pizzagalli Diego A.
Published: June 2019

Background

Theoretical models have emphasized systems-level abnormalities in Major Depressive Disorder (MDD). For unbiased yet rigorous evaluations of pathophysiological mechanisms underlying MDD, it is critically important to develop data-driven approaches that harness whole-brain data to classify MDD and evaluate possible normalizing effects of targeted interventions. Here, using an experimental therapeutics approach coupled with machine-learning we investigated the effect of a pharmacological challenge aiming to enhance dopaminergic signaling on whole-brain’s response to reward-related stimuli in MDD.

Methods

Using a double-blind placebo-controlled design, functional magnetic resonance imaging (fMRI) data from 31 unmedicated MDD participants receiving a single dose of 50 mg amisulpride (MDDAmisulpride), 26 MDD participants receiving placebo (MDDPlacebo), and 28 healthy controls receiving placebo (HCPlacebo) were analyzed. An importance-guided machine learning technique for model selection was used on whole-brain fMRI data probing reward anticipation and consumption to identify features linked to MDD (MDDPlacebo vs. HCPlacebo) and dopaminergic enhancement (MDDAmisulpride vs. MDDPlacebo).

Results

Highly predictive classification models emerged that distinguished MDDPlacebo from HCPlacebo (AUC=0.87) and MDDPlacebo from MDDAmisulpride (AUC=0.89). Although reward-related striatal activation and connectivity were among the most predictive features, the best truncated models based on whole-brain features were significantly better relative to models trained using striatal features only.

Conclusions

Results indicate that, in MDD, enhanced dopaminergic signaling restores abnormal activation and connectivity in a widespread network of regions. These findings provide new insights into the pathophysiology of MDD and pharmacological mechanism of antidepressants at the system level in addressing reward processing deficits among depressed individuals.

ClinicalTrials.gov identifier

NCT01253421 and NCT01701258
Co-localization and confinement of ecto-nucleotidases modulate extracellular adenosine nucleotide pools
Authors: Rahmaninejad Hadi , Pace Tom , Bhatt Shashank , Sun Bin , Kekenes-Huskey Peter M
Published: June 2019

Nucleotides comprise small molecules that perform critical signaling and energetic roles in biological systems. Of these, the concentrations of adenosine and its derivatives, including adenosine tri-, di-, and mono-phosphate are dynamically controlled in the extracellular-space by ecto-nucleotidases that rapidly degrade such nucleotides. In many instances, the close coupling between cells such as those in synaptic junctions yields tiny extracellular 'nanodomains' within which the charged nucleotides interact with densely-packed membranes and biomolecules. While the contributions of electrostatic and steric interactions within such nanodomains are known to shape diffusion-limited reaction rates, less is understood about how these factors control the kinetics of sequentially-coupled ecto-nucleotidase-catalyzed reactions.
To rank the relative importance of these factors, we utilize reaction-diffusion numerical simulations to systematically probe coupled enzyme activity in narrow junctions. We perform these simulations in nanoscale geometries representative of narrow extracellular compartments, within which we localize sequentially- and spatially-coupled enzymes. These enzymes catalyze the conversion of a representative charged substrate such as (ATP) into substrates with different net charges, such as (AMP) and (Ado).
Our modeling approach considers electrostatic interactions of diffusing, charged substrates with extracellular membranes, and coupled enzymes.
With this model, we find that
1) Reaction rates exhibited confinement effects, namely reduced reaction rates relative to bulk, that were most pronounced when the enzyme was close to the pore size and
2) The presence of charge on the pore boundary further tunes reaction rates by controlling the pooling of substrate near the reactive protein akin to ions near trans-membrane proteins.
These findings suggest how remarkable reaction efficiencies of coupled enzymatic processes can be supported in charged and spatially-confined volumes of extracellular spaces.