bluuebunny/crossref_metadata_2025_split huggingface dataset:
Differential loss of effector genes in three recently expanded pandemic clonal lineages of the rice blast fungus
Authors: Latorre Sergio M. , Reyes-Avila C. Sarai , Malmgren Angus , Win Joe , Kamoun Sophien , Burbano Hernán A. 
Published: July 2020

Abstract
Background
Understanding the mechanisms and timescales of plant pathogen outbreaks requires a detailed genome-scale analysis of their population history. The fungus Magnaporthe (Syn. Pyricularia) oryzae—the causal agent of blast disease of cereals— is among the most destructive plant pathogens to world agriculture and a major threat to the production of rice, wheat, and other cereals. Although M. oryzae is a multihost pathogen that infects more than 50 species of cereals and grasses, all rice-infecting isolates belong to a single genetically defined lineage. Here, we combined the two largest genomic datasets to reconstruct the genetic history of the rice-infecting lineage of M. oryzae based on 131 isolates from 21 countries.

Results
The global population of the rice blast fungus consists mainly of three well-defined genetic groups and a diverse set of individuals. Multiple population genetic tests revealed that the rice-infecting lineage of the blast fungus probably originated from a recombining diverse group in Southeast Asia followed by three independent clonal expansions that took place over the last ~ 200 years. Patterns of allele sharing identified a subpopulation from the recombining diverse group that introgressed with one of the clonal lineages before its global expansion. Remarkably, the four genetic lineages of the rice blast fungus vary in the number and patterns of presence and absence of candidate effector genes. These genes encode secreted proteins that modulate plant defense and allow pathogen colonization. In particular, clonal lineages carry a reduced repertoire of effector genes compared with the diverse group, and specific combinations of presence and absence of effector genes define each of the pandemic clonal lineages.

Conclusions
Our analyses reconstruct the genetic history of the rice-infecting lineage of M. oryzae revealing three clonal lineages associated with rice blast pandemics. Each of these lineages displays a specific pattern of presence and absence of effector genes that may have shaped their adaptation to the rice host and their evolutionary history.
Effects of reconstruction techniques after proximal gastrectomy: a systematic review and meta-analysis
Authors: Shaibu Zakari , Chen Zhihong , Mzee Said Abdulrahman Salim , Theophilus Acquah , Danbala Isah Adamu 
Published: July 2020

Abstract
Background
Additional studies comparing several reconstruction methods after proximal gastrectomy have been published; of note, it is necessary to update systematic reviews and meta-analysis from the current evidence-based literature.

Aim
To expand the current knowledge on feasibility and safety, and also to analyze postoperative outcomes of several reconstructive techniques after proximal gastrectomy.

Methods
PubMed, Google Scholar, and Medline databases were searched for original studies, and relevant literature published between the years 1966 and 2019 concerning various reconstructive techniques on proximal gastrectomy were selected. The postoperative outcomes and complications of the reconstructive techniques were assessed. Meta-analyses were performed using Rev-Man 5.0. A total of 29 studies investigating postoperative outcomes of double tract reconstruction, jejunal pouch interposition, jejunal interposition, esophagogastrostomy, and double flap reconstruction were finally selected in the quantitative analysis.

Result
Pooled incidences of reflux esophagitis for double tract reconstruction, jejunal pouch interposition, jejunal interposition esophagogastrostomy, and double flap reconstruction were 8.6%, 13.8%, 13.8%, 19.3%, and 8.9% respectively. Meta-analysis showed a decreased length of hospital in the JI group as compared to the JPI group (heterogeneity: Chi2 = 1.34, df = 1 (P = 0.25); I2 = 26%, test for overall effect: Z = 2.22 (P = 0.03). There was also a significant difference between JI and EG in length of hospital stay with heterogeneity: Chi2 = 1.40, df = 3 (P = 0.71); I2 = 0%, test for overall effect: Z = 5.04 (P < 0.00001). Operative time was less in the EG group as compared to the JI group (heterogeneity: Chi2 = 31.09, df = 5 (P < 0.00001); I2 = 84%, test for overall effect: Z = 32.35 (P < 0.00001).

Conclusion
Although current reconstructive techniques present excellent anti-reflux efficacy, the optimal reconstructive method remains to be determined. The double flap reconstruction proved to lower the rate of complication, but the DTR, JI, JPI, and EG groups showed higher incidence of complications in anastomotic leakage, anastomotic stricture, and residual food. In the meta-analysis result, the complications between the JI, JPI, and EG were comparable but the EG group showed to have better postoperative outcomes concerning the operative time, blood loss, and length of hospital stay.
Feasibility of totally laparoscopic pylorus-preserving gastrectomy with intracorporeal gastro-gastrostomy for early gastric cancer: a retrospective cohort study
Authors: Akiyama Yuji , Sasaki Akira , Iwaya Takeshi , Fujisawa Ryosuke , Sasaki Noriyuki , Nikai Haruka , Endo Fumitaka , Baba Shigeaki , Hasegawa Yasushi , Kimura Toshimoto , Takahara Takeshi , Nitta Hiroyuki , Otsuka Koki , Koeda Keisuke 
Published: July 2020

Abstract
Background
Pylorus-preserving gastrectomy (PPG) has been accepted as a function-preserving surgery for the treatment of early gastric cancer in East Asian countries. Therefore, this study aimed to evaluate the feasibility and safety of totally laparoscopic PPG (TLPPG) with intracorporeal anastomosis.

Methods
A total of 43 patients with early gastric cancer underwent laparoscopy-assisted PPG (LAPPG) with extracorporeal anastomosis between May 2006 and November 2012. The operative outcomes of 22 patients who underwent TLPPG between November 2012 and February 2019 were evaluated, and data were compared with that of the LAPPG group.

Results
No significant difference in the operative time was observed between the two groups. Blood loss was lower in the TLPPG group (18.5 mL) than in the LAPPG group (30.7 mL, p = 0.008), and the length of abdominal incision was shorter in the TLPPG group (3.8 cm) than in the LAPPG group (4.7 cm, p < 0.001). No significant difference in the complication rate was observed between the two groups (13.6% in the TLPPG vs. 9.3% in the LAPPG group, p = 0.594). No anastomosis-related complications occurred in either group. No significant between-group difference was observed in the delayed gastric emptying (TLPPG, 9.1 vs. LAPPG, 7%, p = 0.762). The initiation of postoperative fluid (TLPPG, 1.0 day vs. LAPPG, 3.0 days, p < 0.001) and meal (TLPPG, 3.0 days vs. LAPPG, 4.0 days, p < 0.001) intake was earlier in the TLPPG group than in the LAPPG group. No significant between-group difference was observed in the postoperative hospital stay.

Conclusions
The findings of this study suggest that TLPPG with intracorporeal reconstruction not only is as feasible and safe as LAPPG for the treatment of patients with early gastric cancer but also provides certain advantages such as reduced blood loss and wound size.
YYFZBJS ameliorates colorectal cancer progression in ApcMin/+ mice by remodeling gut microbiota and inhibiting regulatory T-cell generation
Authors: Sui Hua , Zhang Lu , Gu Kaijuan , Chai Ni , Ji Qing , Zhou Lihong , Wang Yan , Ren Junze , Yang Limei , Zhang Bimeng , Hu Jing , Li Qi 
Published: July 2020

AbstractBackgroundProgression of Colorectal cancer (CRC) is influenced by single or compounded environmental factors. Accumulating evidence shows that microbiota can influence the outcome of cancer immunotherapy. T cell, one of the main populations of effector immune cells in antitumor immunity, has been considered as a double-edged sword during the progression of CRC. Our previous studies indicate that traditional Chinese herbs (TCM) have potential anticancer effects in improving quality of life and therapeutic effect. However, little is known about the mechanism of TCM formula in cancer prevention.MethodsHere, we used C57BL/6 JApcMin/+mice, an animal model of human intestinal tumorigenesis, to investigate the gut bacterial diversity and their mechanisms of action in gastrointestinal adenomas, and to evaluate the effects of Yi-Yi-Fu-Zi-Bai-Jiang-San (YYFZBJS) on of colon carcinogenesis in vivo and in vitro. Through human-into-mice fecal microbiota transplantation (FMT) experiments from YYFZBJS volunteers or control donors, we were able to differentially modulate the tumor microbiome and affect tumor growth as well as tumor immune infiltration.ResultsWe report herein, YYFZBJS treatment blocked tumor initiation and progression inApcMin/+mice with less change of body weight and increased immune function. Moreover, diversity analysis of fecal samples demonstrated that YYFZBJS regulated animal’s natural gut flora, includingBacteroides fragilis,Lachnospiraceaeand so on. Intestinal tumors from conventional and germ-free mice fed with stool from YYFZBJS volunteers had been decreased. Some inflammation’ expression also have been regulated by the gut microbiota mediated immune cells. Intestinal lymphatic, and mesenteric lymph nodes (MLN), accumulated CD4+ CD25+ Foxp3 positive Treg cells were reduced by YYFZBJS treatment inApcMin/+mice. Although YYFZBJS had no inhibition on CRC cell proliferation by itself, the altered Tregs mediated by YYFZBJS repressed CRC cancer cell growth, along with reduction of the phosphorylation of β-catenin.ConclusionsIn conclusion, we demonstrated that gut microbiota and Treg were involved in CRC development and progression, and we propose YYFZBJS as a new potential drug option for the treatment of CRC.Graphical abstract
Cardiac stem cell therapy among Clinics of Uncertain Regulatory Status (COURS): under-regulated, under-observed, incompletely understood
Authors: Lindeman Amanda , Pepine Carl J. , March Keith L. 
Published: July 2020

Abstract
Background
Although a large body of information exists relating to cellular therapies, much of this information is either anecdotal or has been obtained from relatively small clinical trials, so that the level of evidence available to direct adoption of therapeutic approaches is quite limited. Despite this, a large number of clinics offer various cellular treatments without having gone through the processes of FDA approval. Florida is considered a “hotspot” of such sites, with a large number of clinics relative to the population.

Methods
To better understand the magnitude and scope of this issue with a specific focus on cardiovascular disease, we surveyed clinics in Florida advertising “cell therapy for heart failure”. We identified only 8 clinics that “treat cardiac conditions, including heart failure.” Data on administration route, cell type used, dose, success rate, cost, and training of persons performing procedures were collected when available, via email, telephone, or website information.

Results
A total of 20,135 patients were identified as treated: 2157 for cardiac conditions. All clinics reported administering cells intravenously, using either adipose- or umbilical-derived sources. Doses ranged from 30 to 150 million cells per treatment. The “success rate” ranged from 65 to 85%, with costs from $6000 to $20,700. Procedures were performed by PAs, MDs, and DOs.

Conclusion
Large numbers of patients (> 10% of all 20,135 patients) have been and presumably are still are being treated for “cardiac conditions.” We conclude that implementation of uniform data collection with an outcome registry, as well as creation of a public database listing FDA-approved cell-based clinical trials, would be useful to patients and the cardiovascular field at large.
Real GDP growth rates and healthcare spending – comparison between the G7 and the EM7 countries
Authors: Jakovljevic Mihajlo , Timofeyev Yuriy , Ranabhat Chhabi Lal , Fernandes Paula Odete , Teixeira João Paulo , Rancic Nemanja , Reshetnikov Vladimir 
Published: July 2020

Abstract
Background
Accelerated globalisation has substantially contributed to the rise of emerging markets worldwide. The G7 and Emerging Markets Seven (EM7) behaved in significantly different macroeconomic ways before, during, and after the 2008 Global Crisis. Average real GDP growth rates remained substantially higher among the EM7, while unemployment rates changed their patterns after the crisis. Since 2017, however, approximately one half of the worldwide economic growth is attributable to the EM7, and only a quarter to the G7. This paper aims to analyse the association between the health spending and real GDP growth in the G7 and the EM7 countries.

Results
In terms of GDP growth, the EM7 exhibited a higher degree of resilience during the 2008 crisis, compared to the G7. Unemployment in the G7 nations was rising significantly, compared to pre-recession levels, but, in the EM7, it remained traditionally high. In the G7, the austerity (measured as a percentage of GDP) significantly decreased the public health expenditure, even more so than in the EM7. Out-of-pocket health expenditure grew at a far more concerning pace in the EM7 compared to the G7 during the crisis, exposing the vulnerability of households living close to the poverty line. Regression analysis demonstrated that, in the G7, real GDP growth had a positive impact on out-of-pocket expenditure, measured as a percentage of current health expenditure, expressed as a percentage of GDP (CHE). In the EM7, it negatively affected CHE, CHE per capita, and out-of-pocket expenditure per capita.

Conclusion
The EM7 countries demonstrated stronger endurance, withstanding the consequences of the crisis as compared to the G7 economies. Evidence of this was most visible in real growth and unemployment rates, before, during and after the crisis. It influenced health spending patterns in both groups, although they tended to diverge instead of converge in several important areas.
Semantic segmentation to identify bladder layers from H&E Images
Authors: Niazi Muhammad Khalid Khan , Yazgan Enes , Tavolara Thomas E. , Li Wencheng , Lee Cheryl T. , Parwani Anil , Gurcan Metin N. 
Published: July 2020

Abstract
Background
Identification of bladder layers is a necessary prerequisite to bladder cancer diagnosis and prognosis. We present a method of multi-class image segmentation, which recognizes urothelium, lamina propria, muscularis propria, and muscularis mucosa layers as well as regions of red blood cells, cauterized tissue, and inflamed tissue from images of hematoxylin and eosin stained slides of bladder biopsies.

Methods
Segmentation is carried out using a U-Net architecture. The number of layers was either, eight, ten, or twelve and combined with a weight initializers of He uniform, He normal, Glorot uniform, and Glorot normal. The most optimal of these parameters was found by through a seven-fold training, validation, and testing of a dataset of 39 whole slide images of T1 bladder biopsies.

Results
The most optimal model was a twelve layer U-net using He normal initializer. Initial visual evaluation by an experienced pathologist on an independent set of 15 slides segmented by our method yielded an average score of 8.93 ± 0.6 out of 10 for segmentation accuracy. It took only 23 min for the pathologist to review 15 slides (1.53 min/slide) with the computer annotations. To assess the generalizability of the proposed model, we acquired an additional independent set of 53 whole slide images and segmented them using our method. Visual examination by a different experienced pathologist yielded an average score of 8.87 ± 0.63 out of 10 for segmentation accuracy.

Conclusions
Our preliminary findings suggest that predictions of our model can minimize the time needed by pathologists to annotate slides. Moreover, the method has the potential to identify the bladder layers accurately. Further development can assist the pathologist with the diagnosis of T1 bladder cancer.
Establishing cross-systems collaborations for implementation: protocol for a longitudinal mixed methods study
Authors: Bunger Alicia C. , Chuang Emmeline , Girth Amanda , Lancaster Kathryn E. , Gadel Fawn , Himmeger Marla , Saldana Lisa , Powell Byron J. , Aarons Gregory A. 
Published: July 2020

AbstractBackgroundCross-system interventions can help integrate services across different service delivery systems but require organizations to establish strong collaborative relationships for implementation. Contingency theory suggests that the effectiveness of different collaborative strategies (i.e. specific ways organizations align operations and services) varies by context. This paper describes a study of different strategies for fostering collaboration between child welfare and substance abuse treatment agencies and the conditions under which they are effective for implementation. We also describe the development and piloting of the Collaborating Across Systems for Program Implementation (CASPI) tool—a decision-making guide intended to help researchers and organizational leaders identify and use appropriate collaborative strategies for their context.Methods/designThis multisite longitudinal, mixed methods study, leverages a naturally occurring implementation initiative -- in up to 17 Ohio counties -- to implement Ohio START (Sobriety Treatment and Reducing Trauma). START is a child welfare model that requires strong collaboration with local substance use treatment organizations to promote integrated services. During the first two years, we will identify collaborative strategies associated with improved START implementation (penetration and fidelity) and service delivery outcomes (timeliness), given system, and organizational features. We will conduct a convergent mixed methods study drawing on worker surveys, agency documents, administrative data, formal partner agreements, and group interviews. Data will be integrated and analyzed using Qualitative Comparative Analysis (QCA). To develop the CASPI, an expert panel comprised of implementation experts, and community stakeholders will convene to synthesize our findings and develop contents (including a decision tree). During the final year of the study, we will assess the acceptability, appropriateness, and feasibility of the CASPI in a randomized vignette experiment, and a pilot-test with 3 child welfare agencies that have not yet implemented START.DiscussionOur results will lay the groundwork for a larger controlled trial that will test the CASPI’s effectiveness for supporting effective and efficient implementation of cross-system interventions like START. The CASPI is expected to help leaders and researchers select and use collaboration strategies tailored to their context and be applicable in a wide range of settings including rural communities. Our work also advances system-level implementation strategies.Trial registrationNCT03931005, Registered April 29, 2019.
Process evaluation of a complex intervention to promote advance care planning in community-dwelling older persons (the STADPLAN study)—study protocol
Authors: Silies Katharina , Schnakenberg Rieke , Berg Almuth , Kirchner Änne , Langner Henriette , Köberlein-Neu Juliane , Meyer Gabriele , Hoffmann Falk , Köpke Sascha 
Published: July 2020

Abstract
Background
Process evaluation addresses the implementation, mechanisms of impact, and context of participants in complex interventions. The STADPLAN study assesses the effects of conversations on advance care planning (ACP) led by trained nurse facilitators. The complex intervention consists of several components that may lead to various changes in attitude and behavior regarding personal ACP activities. With the process evaluation, we aim to assess how changes were achieved in the STADPLAN intervention.

Methods
The planned process evaluation study will be conducted alongside a cluster-randomized controlled trial on ACP in home care services (HCS). Trained nurse facilitators will deliver the ACP intervention consisting of an information brochure and two ACP conversations. A logic model depicts the assumed change processes of the intervention: the educational program enables nurses to conduct ACP conversations with patients and their caregivers. Patients gain knowledge and reflect upon and engage in their own ACP. Caregivers better understand patients’ wishes and feel reassured in their role as surrogates. Designation of a surrogate and communication on ACP are facilitated. We will assess the effects of the educational program with questionnaires and a focus group including all participating nurses. We will measure ACP engagement, and prevalence of advance directives in patients, and ask for their experiences with the intervention. We will conduct semi-structured interviews with caregivers about their expectations and experiences regarding ACP in general and the intervention. We will address context factors, e.g., basic characteristics of the HCS (such as ownership, number of clients, staff and qualification). Analysis will be based upon the logic model, integrating qualitative and quantitative data.

Discussion
The comprehensive process evaluation will provide essential information on the feasibility of implementation strategies and the clinical relevance of a nurse-led ACP intervention in home care recipients and its generalizability and transferability to other settings.

Trial registration
German Clinical Trials Register: DRKS00016886. Registered retrospectively on June 4, 2019, first participant included on May 29, 2019.
Pullback attractors of nonautonomous discrete p-Laplacian complex Ginzburg–Landau equations with fast-varying delays
Authors: Pu Xiaoqin , Wang Xuemin , Li Dingshi 
Published: July 2020

AbstractIn this paper, we consider a class of nonautonomous discrete p-Laplacian complex Ginzburg–Landau equations with time-varying delays. We prove the existence and uniqueness of pullback attractor for these equations. The existing results of studying attractors for time-varying delay equations require that the derivative of the delay term should be less than 1 (called slow-varying delay). By using differential inequality technique, our results remove the constraints on the delay derivative. So, we can deal with the equations with fast-varying delays (without any constraints on the delay derivative).