bluuebunny/crossref_metadata_2025 huggingface dataset:
Unilateral live twin tubal ectopic pregnancy presenting at 12 weeks of gestation
Authors: Seak Chen-June , Goh Zhong Ning Leonard , Wong Alexis Ching , Seak Joanna Chen-Yeen , Seak Chen-Ken
Published: October 2019

Rationale

Abdominal pain in pregnancy represents a demanding diagnostic challenge in the emergency department (ED) due to the extensive list of differential diagnoses to be considered, coupled with the possibility of each disease having nonclassical, atypical signs and symptoms, resultant from the patient's pregnant state. Additionally, emergency physicians (EPs) face limitations on investigative imaging modalities because of the need to minimize fetal radiation exposure. EPs have to tackle this diagnostic challenge while performing a balancing act to maximize both maternal and fetal outcomes in a time-sensitive manner, becauser any delays in decision-making at the ED may threaten the safety of mother and child. Two common causes of abdominal pain in pregnancy presenting to the ED are acute appendicitis and ectopic pregnancy. The latter is almost always diagnosed by 10 weeks of gestation. Here, we report an extremely rare case of unilateral live spontaneous twin tubal ectopic pregnancy presenting past 12 weeks of gestation, diagnosed after magnetic resonance imaging (MRI) of the abdomen.

Patient concerns

A 37-year-old gravida 2 para 1 at 12 weeks and 6 days of gestation presented to our ED with a 2-day history of right iliac fossa pain, not associated with vaginal bleeding, fever, diarrhea, and vomiting. On examination, she was tachycardic (pulse rate 124 beats/min) and hypertensive (blood pressure 142/88 mm Hg). There was marked tenderness and guarding at the lower abdomen.

Diagnoses

Blood investigations were unremarkable, while abdominal ultrasonography found a live twin gestation with foetal heartbeats of 185 and 180 beats/min. MRI of the abdomen revealed an empty uterine cavity; 2 amniotic sacs and fetuses of diameter 10 cm, and a single placenta were noted in the right uterine adnexa. The patient was diagnosed with right live monochorionic diamniotic twin tubal pregnancy.

Intervention

Our patient underwent emergency laparoscopic right salpingectomy.

Outcomes

The operation was successful and her postoperative care remained uneventful up to discharge.

Lessons

Ectopic pregnancy cannot be ruled out based on prior normal antenatal examinations and gestational age of >10 weeks. EPs should not hesitate to order MRI scans for further evaluation if ultrasonography and laboratory findings are equivocal.
Effect of physical therapy for chronic obstructive pulmonary disease
Authors: Gao Hui , Gao Yuan , Sun Ping , Shen Jie , Yao Hui-juan , Fu Shi-dong , Meng Cheng
Published: October 2019

Background:

Previous studies have reported that physical therapy (PT) can be used for the treatment of chronic obstructive pulmonary disease (COPD). However, its effectiveness is still inconclusive. This systematic review will aim to assess its effectiveness and safety for the treatment of patients with COPD.

Methods:

All randomized controlled trials (RCTs) literatures of PT for COPD will be searched from the databases of Cochrane Central Register of Controlled Trials (CENTRAL), EMBASE, MEDILINE, Web of Science, Cumulative Index to Nursing and Allied Health Literature, Allied and Complementary Medicine Database, Chinese Biomedical Literature Database, China National Knowledge Infrastructure, VIP Information, and Wanfang Data from inception to the present without any language restrictions. Two reviewers will independently perform the study selection, data extraction, and methodological quality assessment. A third reviewer will be invited to resolve any disagreements occurred between 2 reviewers.

Results:

The primary outcome is lung function. The secondary outcomes include symptoms, health-related quality of life, mortality, and adverse events. The outcome data will be pooled by using the models of random-effects or fixed-effects according to the detected heterogeneity.

Conclusion:

The findings of this study will provide up-todated summary evidence for assessing the effectiveness and safety of PT for COPD.
Efficacy of blood purification for severe pancreatitis and acute respiratory distress syndrome
Authors: Jin Yi-hua , Liu Yang
Published: October 2019

Background:

This study will assess the efficacy and safety of blood purification (BP) for severe pancreatitis (SP) and acute respiratory distress syndrome (ARDS).

Methods:

We will search the following electronic databases of Ovid MEDLINE, EMBASE, Web of Science, Cochrane Library, Scopus, Cumulative Index to Nursing and Allied Health Literature, the Allied and Complementary Medicine Database, Chinese Biomedical Literature Database, China National Knowledge Infrastructure, and WANGFANG from inception to the present without language restriction. A systematic review and data synthesis will be carried out of randomized controlled trials of BP for the treatment of patients with SP and ARDS. RevMan 5.3 software will be used for statistical analysis.

Results:

This systematic review will evaluate the efficacy and safety of BP for the treatment of patients with SP and ARDS. The primary outcome includes respiratory indexes, blood biochemical and inflammatory factors. The secondary outcomes consist of complications, sepsis, abdominal hemorrhage, renal failure, length of hospital stay, and mortality.

Conclusion:

This study will provide up-to-date evidence of BP for the treatment of patients with SP and ARDS.

PROSPERO registration number:

PROSPERO CRD42019139467.
Bone health in adult trans persons: an update of the literature
Authors: Wiepjes Chantal M. , den Heijer Martin , T'Sjoen Guy G.
Published: October 2019

Purpose of review

Hormonal treatment in trans persons can affect bone health. In this review, recent studies published on this topic in adults are discussed.

Recent findings

Before starting hormonal treatment, trans women were found to have lower bone mineral density than cis men, which seems to be related to lower vitamin D concentrations and lower lean body mass, whereas this was not found in trans men. Short-term and long-term studies show that hormonal treatment does not have detrimental effects on bone mineral density in trans women and trans men. Low estradiol concentrations were associated with a decrease in bone mineral density in trans women.

Based on the reassuring findings in these studies, regularly assessing bone mineral density during hormonal treatment does not seem necessary. This confirms the Endocrine Society Guideline stating that bone mineral density should be measured only when risk factors for osteoporosis exist, especially in people who stop hormonal treatment after gonadectomy. The relationship with estradiol concentrations indicate that hormone supplementation should be adequate and therapy compliance should be stimulated. As vitamin D deficiency frequently occurs, vitamin D supplementation should be considered. Future research should focus on fracture risk and long-term changes in bone geometry.
Older Adults’ Perspectives of End of Life After the Death of a Significant Other
Authors: Sopcheck Janet
Published: October 2019

Many older adults have experienced the death of a significant other. Understanding their perspectives from this past experience may heighten nursing insights about the type of care they desire at the end of their lives. The aim of this secondary analysis was to describe how the death of a significant other influenced older adults’ perspectives about their end of life. Fifteen older adults residing in a continuing care retirement community participated in the primary study that explored the challenge of losing a loved one. Inductive content analysis was used to derive 4 themes to explain their perspectives about end of life: peacefully slip away—no heroics, familiarity—making plans that stick, tying up loose ends—what’s left to do, and accepting—my time is up. This study’s findings imply that nurses, with medical providers, should openly discuss with older adults their end-of-life concerns and care desired. Clinicians should receive education such as the COMFORT conversation and End-of-Life Nursing Education Consortium courses. Further research should explore whether older adults may be more encouraged to formulate advance directives after the death of significant others and end-of-life issues in retirement communities. Increasing public awareness of palliative and hospice services is needed.
Treatment options for patients with mantle cell lymphoma post-transplantation
Authors: Cowley Emily C. , McFarlane Thomas R.
Published: October 2019

Mantle cell lymphoma is a rare subtype of B-cell lymphoma which carries with it a poor prognosis and is typically refractory to treatment. Autologous stem cell transplant (ASCT) has been shown to improve survival, but is not considered curative. There is currently no specific preferred regimen of treatment according to current guidelines for patients who fail ASCT. We undertook a systematic scoping review to examine the existing literature in this setting. A total of 3045 records were screened, yielding 40 full-text articles, 12 of which were included in the results. Ibrutinib and venetoclax appeared to produce the highest response rates and length of progression-free survival post-ASCT, however, there are serious gaps in the literature regarding what is actually known about the efficacy of treatment regiments for relapsed/refractory mantle cell lymphoma in post-ASCT patients and more randomized, controlled clinical trials are needed in this area.
Significance of the Marginal Mandibular Branch in Relation to Facial Palsy Reconstruction
Authors: Mandlik Veronika , Ruewe Marc , Engelmann Simon , Geis Sebastian , Taeger Christian , Kehrer Michael , Tamm Ernst R. , Bleys Ronald , Prantl Lukas , Kehrer Andreas
Published: October 2019

Background

The marginal mandibular branch (MMB) of the facial nerve provides lower lip symmetry apparent during human smile or crying and is mandatory for vocal phonation. In treating facial palsy patients, so far, little attention is directed at the MMB in facial reanimation surgery. However, isolated paralysis may occur congenital, in Bell's palsy or iatrogenic during surgery, prone to its anatomical course. A variety of therapies address symmetry with either weakening of the functional side or reconstruction of the paralyzed side. To further clarify the histoanatomic basis of facial reanimation procedures using nerve transfers, we conducted a human cadaver study examining macroanatomical and microanatomical features of the MMB including its axonal capacity.

Methods

Nerve biopsies of the MMB were available from 96 facial halves. Histological processing, digitalization, nerve morphometry investigation, and semiautomated axonal quantification were performed. Statistical analysis was conducted with P < 0.05 as level of significance.

Results

The main branch of 96 specimens contained an average of 3.72 fascicles 1 to 12, and the axonal capacity was 1603 ± 849 (398–5110, n = 85). Differences were found for sex (P = 0.018), not for facial sides (P = 0.687). Diameters were measured with 1130 ± 327 μm (643–2139, n = 79). A significant difference was noted between sexes (P = 0.029), not for facial sides (P = 0.512.) One millimeter in diameter corresponded to 1480 ± 630 axons (n = 71). A number of 900 axons was correlated with 0.97 mm (specificity, 90%; sensitivity, 72%).

Conclusions

Our morphometric results for the MMB provide basic information for further investigations, among dealing with functional reconstructive procedures such as nerve transfers, nerve grafting for direct neurotization or babysitter procedures, and neurectomies to provide ideal power and authenticity.
Surgical Quality Assurance in COLOR III
Authors: Tsai Alice Y-C. , Mavroveli Stella , Miskovic Danilo , van Oostendorp Stefan , Adamina Michel , Hompes Roel , Aigner Felix , Spinelli Antonino , Warusavitarne Janindra , Knol Joep , Albert Matthew , Nassif George , Bemelman Willem , Boni Luigi , Ovesen Henrik , Austin Ralph , Muratore Andrea , Seitinger Gerald , Sietses Colin , Lacy Antonio M. , Tuynman Jurriaan B. , Bonjer H. Jaap , Hanna George B.
Published: October 2019

Objective:

The aim of this study was to develop an objective and reliable surgical quality assurance system (SQA) for COLOR III, an international multicenter randomized controlled trial (RCT) comparing transanal total mesorectal excision (TaTME) with laparoscopic approach for rectal cancer.

Background of Summary Data:

SQA influences outcome measures in RCTs such as lymph nodes harvest, in-hospital mortality, and locoregional cancer recurrence. However, levels of SQA are variable.

Method:

Hierarchical task analysis of TaTME was performed. A 4-round Delphi methodology was applied for standardization of TaTME steps. Semistructured interviews were conducted in round 1 to identify key steps and tasks, which were rated as mandatory, optional, or prohibited in rounds 2 to 4 using questionnaires. Competency assessment tool (CAT) was developed and its content validity was examined by expert surgeons. Twenty unedited videos were assessed to test reliability using generalizability theory.

Results:

Eighty-three of 101 surgical tasks identified reached 70% agreement (26 mandatory, 56 optional, and 1 prohibited). An operative guide of standardized TaTME was created. CAT is matrix of 9 steps and 4 performance qualities: exposure, execution, adverse event, and end-product. The overall G-coefficient was 0.883. Inter-rater and interitem reliability were 0.883 and 0.986. To enter COLOR III, 2 unedited TaTME and 1 laparoscopic TME videos were submitted and assessed by 2 independent assessors using CAT.

Conclusion:

We described an iterative approach to develop an objective SQA within multicenter RCT. This approach provided standardization, the development of reliable and valid CAT, and the criteria for trial entry and monitoring surgical performance during the trial.
A Survey of Current Procurement Travel Practices, Accident Frequency, and Perceptions of Safety
Authors: Schenk Austin D. , Washburn William K. , Adams Andrew B. , Lynch Raymond J.
Published: October 2019

Background.

In 2018, 81% of the 36, 529 solid organs transplanted in the United States came from deceased donors. These organs were recovered through widespread use of aeromedical and emergency ground transportation systems. Urgently scheduled travel to remote hospitals at night and in varied weather conditions carries risk for the transplant professionals involved. A landmark survey conducted in 2007 demonstrated that 80% of respondents had experienced a “near-miss” event while on a procurement trip, and 15% had been involved in at least 1 accident. One decade later, we sought to revisit the issue of procurement related travel safety.

Methods.

A 32 question survey designed to interrogate travel practice, accident frequency, and perceptions of safety was sent to the American Society of Transplant Surgeons membership.

Results.

Our survey response rate was 20.6%. At least 1 travel accident with bodily injury was reported by 23% of respondents and yet only 7% of respondents reported feeling “unsafe” or “very unsafe” during procurement travel. Sixteen percent of respondents participated in a procurement at a dedicated organ procurement facility, and only 53% of procurement surgeons completed at least 1 deceased donor procurement at their own hospital facility within the preceding 12 months.

Conclusions.

In a field where increasingly aggressive organ utilization is the norm, the efficiency and safety of procurement travel merits ongoing consideration. Addressing these concerns takes on new significance as organ allocation policies change geographic distribution to expand the extent of travel required for surgical teams.
Fastidious anaerobe agar (FAA) as a suitable medium for antimicrobial susceptibility testing (AST) of anaerobes by agar dilution
Authors: Copsey-Mawer Sarah , Scotford Selina , Copsey-Mawer Bethan , Davis Carol , Perry Michael , Morris Trefor , Hughes Harriet
Published: October 2019

Background

Agar dilution is the reference method for antimicrobial susceptibility testing (AST) of anaerobes, but currently the only verified and published method utilises supplemented brucella agar, which is not readily available in the UK.

As FAA is often the medium of choice for primary culture of anaerobes in clinical laboratories, the aim of this study was to investigate the suitability of this medium as an alternative to brucella agar for the reference method.

Methods

One hundred isolates submitted to the UKARU, all with pre-determined MICs to: clindamycin; meropenem; metronidazole; penicillin and doxycycline, were tested.

MICs were obtained by agar dilution using both in-house produced FAA, supplemented with 5% defibrinated horse blood, and supplemented brucella blood agar (BRU).

End points were selected according to CLSI guidance and interpreted using EUCAST clinical breakpoints for anaerobes (FDA guidance for doxycycline).

Results

For the majority of isolates the correlation between FAA and BRU MICs was good.

Errors were found for each antimicrobial, with the highest numbers recorded for metronidazole and doxycycline. The majority of errors were within 1-2 dilutions, but spanned the clinical breakpoints. Others were single replicate errors, which were anomalous against a minimum of three additional results.

Several species such as P. distasonis and C. ramosum demonstrated raised numbers of errors/ variable results and will require further investigation.

Conclusions

Overall the reproducibility of agar dilution testing on FAA compared to BRU was good, suggesting that FAA is a suitable media for AST of anaerobes. Further assessment of several species is required.
Diversity of the class Coriobacteriia within different ecosystems
Authors: Hoyles Lesley
Published: October 2019

Members of the class Coriobacteriia are little studied, important fastidious anaerobes within the human gut microbiota. Collinsella aerofaciens is a core member of the gut microbiota that can present several different fermentation profiles within individuals, while Eggerthella lenta is implicated in xenobiotic metabolism. Recent ‘culturomics’ studies have greatly increased the number of Coriobacteriia recovered from human-associated samples, with the names of nine novel genera comprising 12 species published to date. However, the ecological range and genomic diversity of the class Coriobacteriia are poorly understood. Taxonomic assignments within the class Coriobacteriia are unclear, limiting the ways in which data from 16S rRNA gene-based diversity studies in humans and rodent models are interpreted.

Whole-genome and 16S rRNA gene sequences of members of the class Coriobacteriia were analysed and assigned to the families Atopobiaceae, Coriobacteriaceae and Eggerthellaceae. Inconsistencies between 16S rRNA gene sequence and whole genome sequence data deposited in public databases were identified. Newly annotated data searched against 85,000 16S rRNA gene sequence datasets included in the IMNGS (Integrated Microbial Next Generation Sequencing) database demonstrates humans and rodents harbour distinct Coriobacteriia populations. Members of the family Coriobacteriaceae predominate in the human gut, while Eggerthellaceae are more representative of the rodent gut. Metabolic capabilities of the three families of Coriobacteriia vary greatly, with Eggerthellaceae asaccharolytic compared with Coriobacteriaceae and Atopobiaceae. Correct annotation of Coriobacteriia in 16S rRNA gene (and by extension shotgun metagenomic) datasets is required to determine the contributions of these increasingly important bacteria to different ecosystems.
Using PCR in place of GDH as the first line assay in a two-step CDI testing algorithm – evidence of help not hindrance from samples processed at clinical microbiology laboratories in Wales
Authors: Perry Michael , Anderson Bethan , Perry Selina , Graham Lee , Gilbert Lauren , Birchley Alec , Copsey Sarah , Morris Trefor
Published: October 2019

Background

Guidance recommends the use of a two-stage algorithm for diagnosis of Clostridioides difficile infection (CDI) utilising either PCR or a glutamate dehydrogenase (GDH) assay as the first line screen. There is ongoing debate as to whether PCR is a hindrance due to fear of over-diagnosis.

Methods

Between December 2017 and March 2019 over 65,000 tests for CDI were undertaken in Wales. PCR (Serosep EntericBio C. difficile assay) was employed as the first line test for 36% of samples with the remainder tested using a GDH assay (Techlab C. diff ChekTM -60). Positive samples were tested using a toxin EIA (Techlab Tox A/B Quik Chekò). Culture (alcohol shock & CCEY; Oxoid) and capillary electrophoresis PCR ribotyping were undertaken at the UK Anaerobe Reference Unit (UKARU).

Results

The proportion of samples testing positive using PCR and GDH was 5.2% and 8.3% with a toxin EIA positive percentage of 30% and 25% respectively. Of these samples 73% (n=2543) of GDH and 80% (n=974) of PCR positive samples were referred for culture and ribotyping.

No C. difficile was isolated from 15% of GDH and 10.5% of PCR positive specimens. Non-toxigenic strains were isolated from 6.6% of GDH and 0.2% of PCR positive samples and approximately equal proportions of both GDH and PCR positive samples were ribotyped (60% vs. 63% of 2125 samples).

Conclusions

There was no evidence of increased ascertainment of CDI using PCR. In fact, culture and ribotyping demonstrated an improved specificity for PCR that is helpful for accurate CDI diagnosis.
Evaluation of MICROANAUT-S Anaerobes MIC broth microdilution panels for antibiotic susceptibility testing of anaerobes
Authors: Cordovana Miriam , Ambretti Simone
Published: October 2019

Background

Accurate and routine-friendly methods for MIC determination of anaerobes are demanded. Here, we evaluate the performance of a commercially available microdilution panel in comparison to a gradient MIC Strip test.

Methods

N=163 anaerobes clinical isolates (60 species, 23 genera) were tested with the MICRONAUT-S Anaerobes MIC panel (MERLIN Diagnostika, Germany). The same bacterial suspension was used for the panel inoculum, and for testing by MIC Strips (Liofilchem, Italy). The panels were incubated at 37 °C in anaerobic conditions for ≥24 h, and read visually. In case of no bacterial growth for the growth control, incubation was prolonged to 48-72 h. Results were interpreted according to EUCAST guidelines. Comparison was performed in terms of essential agreement, category agreement and error rates.

Results

Category agreement with MIC strips resulted overall 95% (from 95.6% to 100%). Essential agreement resulted 91.1% for piperacillin/tazobactam, and 95% for all the otherantibiotics.Overall, n=15 minor errors, n=2 major errors and n=5 very major errors were observed. For doxycycline, tigecycline and moxifloxacin (for which no breakpoints are available), MICRONAUT results diverged for ≤1 dilution fold from MIC Strips results. For most isolates (117/163) the panels were readable after overnight incubation, in 42 cases after 48 h, in 4 cases after 72 h.

Conclusions

The MICRONAUT-S Anaerobes MIC panels proved to be a reliable microdilution method for antibiotic susceptibility testing of anaerobes, providing results consistent with gradient methodology, with both fast and slow growing species. The ease-of-handling and -result interpretation makes this method suitable for routine implementation.
Improving the surveillance of antimicrobial resistance trends amongst anaerobic oral pathogens
Authors: Thomas Dafydd , Scotford Selina , Thomas James , Crossland James , Kelly Grace , Morris Trefor , Lewis Michael , Wilson Melanie
Published: October 2019

Background

Orofacial infections when treated by dental practitioners are not routinely sampled for culture and susceptibility testing. Consequently, antimicrobial resistant rates amongst the causative bacteria are unknown, hindering efforts to appropriately manage these infections and undertake surveillance of resistant rates. As part of the Cardiff health board leadership in patient safety quality improvement programme a multidisciplinary group was tasked with the aim of improving sampling practices.

Methods

Dental professionals' limited knowledge regarding the role of diagnostic support and an associated lack of confidence in sampling procedures was addressed by the creation and distribution of training aids. Sampling and transportation kits were developed and transport routes identified enabling dentists within the community setting to send samples to the specialist microbiology services based at Cardiff University Dental Hospital [UDH]. All significant anaerobes were identified and antibiotic susceptibility testing undertaken via agar dilution through referral of isolates to the UK Anaerobic Reference Unit.

Results

A 10% increase was seen in the proportion of pus aspirates being received in comparison to pus swabs. For the first time, pus aspirate samples have been received from community dental clinics. A vast diversity of anaerob species and susceptibility profiles have been identified. Increasing rates of resistance amongst Prevotella species to amoxicillin and clindamycin is of concern.

Conclusion

This project has shown that through educational interventions and support the barriers to the sampling of orofacial infections can be overcome. The ultimate aim is for all dentists in Wales to have access to diagnostic support.
Discovering a novel resistance gene for carbapenem resistance in Parabacteroides timonensis using Whole Genome Sequencing
Authors: Boiten Kathleen , Veloo Alida
Published: October 2019

Up to 95% of the human microbiome consists of anaerobic bacteria. However, they are not as well studied as the aerobic bacteria. Among all anaerobes, the Bacteroides group is the best known and most studied. There has been an increase in carbapenem resistance in Bacteroidales strains without a known cause.

We isolated a Parabacteroides timonensis strain, related to Bacteroides, resistant for amoxicillin, clindamycin and meropenem.

The strain was sequenced using the Miseq (Illumina, San Diego, CA), followed by a de novo assembly using CLC workbench to create a draft genome. Resistance genes were detected with ResFinder (https://cge.cbs.dtu.dk/services/ResFinder/). Genome annotation was performed by RAST (http://rast.nmpdr.org/). Protein modeling was performed, on genes of interest, using Phyre2 (http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index) and 3DLigandSite (http://www.sbg.bio.ic.ac.uk/3dligandsite/). FatCat (http://fatcat.burnham.org/) was used to do a pairwise structure alignment to compare protein structures.

The draft genome had a size of 6,356,323 bp, present on 95 contigs. Using Resfinder 1 resistance gene was found, tetQ. A possible novel resistance gene for a metallo β-lactamase related to cfiA was found using RAST. The protein model showed similarities with the model for cfiA and includes several Zn2+ ions, used by metallo β-lactamase to hydrolyze carbapenems.

Our results indicate the presence of a not yet described metallo β-lactamase. There are also indications that a conjugative transposon is present, enabling horizontal gene transfer. No erm genes, encoding for clindamycin resistance, were detected in the draft genome.
Faster diffusive dynamics of histone-like nucleoid structuring proteins in live bacteria caused by silver ions
Authors: Sadoon Asmaa A. , Khadka Prabhat , Freeland Jack , Gundampati Ravi Kumar , Manso Ryan , Ruiz Mason , Krishnamurthi Venkata R. , Thallapuranam Suresh Kumar , Chen Jingyi , Wang Yong
Published: October 2019

The antimicrobial activity and mechanism of silver ions (Ag+) have gained broad attention in recent years. However, dynamic studies are rare in this field. Here, we report our measurement of the effects of Ag+ ions on the dynamics of histone-like nucleoid structuring (H-NS) proteins in live bacteria using single-particle tracking photoactivated localization microscopy (sptPALM). It was found that treating the bacteria with Ag+ ions led to faster diffusive dynamics of H-NS proteins. Several techniques were used to understand the mechanism of the observed faster dynamics. Electrophoretic mobility shift assay on purified H-NS proteins indicated that Ag+ ions weaken the binding between H-NS proteins and DNA. Isothermal titration calorimetry confirmed that DNA and Ag+ ions interact directly. Our recently developed sensing method based on bent DNA suggested that Ag+ ions caused dehybridization of double-stranded DNA (i.e., dissociation into single strands). These evidences led us to a plausible mechanism for the observed faster dynamics of H-NS proteins in live bacteria when subjected to Ag+ ions: Ag+-induced DNA dehybridization weakens the binding between H-NS proteins and DNA. This work highlighted the importance of dynamic study of single proteins in the live cells for understanding the functions of antimicrobial agents to the bacteria.
Does extrinsic mortality accelerate the pace of life? A bare-bones approach
Authors: André Jean-Baptiste , Rousset François
Published: October 2019

1

It is commonly asserted that when extrinsic mortality is high, individuals should invest early in reproduction. This intuition thrives in the literature on life-history theory and human behavior, yet it has been criticized repeatedly on the basis of mathematical models. The intuition is indeed wrong; but a recent theoretical criticism has confused the reason why it is wrong, thereby obscuring earlier and sounder criticisms. In the present article, based on the simplest possible model, we sought to clarify these issues. We confirm earlier findings that extrinsic mortality can affect the evolution of pace of life, not because it leaves little time to reproduce, but through its effects on density-dependent competition. This result highlights the importance of accounting for density-dependence in theoretical models and data analyses. Further, we find little support for the recent claim that the direction of selection on a reaction norm in a variable environment cannot be easily inferred from models made in homogeneous environments. In conclusion, although life-history theory is still imperfect, it has provided simple results that deserve to be understood.
RNA-Seq analysis reveals pluripotency-associated genes and their interaction networks in human embryonic stem cells
Authors: Ghosh Arindam , Som Anup
Published: October 2019

Insight into the key genes of pluripotency in human and their interrelationships is necessary for understanding the underlying mechanism of pluripotency and hence their successful application in regenerative medicine. The recent advances in transcriptomics technologies have created new opportunities to decipher the genes involved in pluripotency, genetic network that governs the unique properties of embryonic stem cells and lineage differentiation mechanisms in a deeper scale. There are a large number of experimental studies on human embryonic stem cells (hESCs) being routinely conducted for unfolding the underlying biology of embryogenesis and their clinical prospects. However, the outcome of these studies often lacks consensus due to differences in samples, experimental techniques and/or analysis protocols. A universal stemness gene list is still lacking. In this quest, we compared transcriptomic profiles of pluripotent and non-pluripotent samples from diverse cell lines/types generated through RNA-sequencing (RNA-seq). We used a uniform pipeline for the analysis of raw RNA-seq data in order to reduce the amount of variation. Our analysis revealed a consensus set of 498 pluripotency-associated genes and 432 genes as potential pluripotent cell differentiation markers. Furthermore, we predicted 32 genes as "pluripotency critical genes". Reconstruction and analysis of co-expression networks further highlighted the importance of these genes. Gene ontology (GO) and pathway enrichment analysis, StemChecker and literature survey confirmed the involvement of the genes in the induction and maintenance of pluripotency, though more experimental studies are required for understanding their molecular mechanisms in human.
Season-specific carry-over of early-life associations in a monogamous bird species
Authors: Kurvers Ralf H.J.M. , Prox Lea , Farine Damien R. , Jongeling Coretta , Snijders Lysanne
Published: October 2019

Social relationships can have important fitness consequences. Although there is increasing evidence that social relationships carry over across contexts, few studies have investigated whether relationships formed early in life are carried over to adulthood. For example, juveniles of monogamous species go through a major life-history stage transition—pair formation—during which the pair bond becomes a central unit of the social organization. At present, it remains unclear if pair members retain their early-life relationships after pair formation. We investigated whether same-sex associations formed early in life carry over into adulthood and whether carry-over was dependent on season, in a monogamous species. Moreover, we investigated the role of familiarity, genetic relatedness and aggression on the perseverance of social associations. We studied the social structure before and after pair formation in captive barnacle geese (Branta leucopsis), a highly social, long-lived, monogamous species. We constructed association networks of groups of geese before pair formation, during the subsequent breeding season, and in the following wintering season. Next, we studied how these associations carried over during seasonal changes. We found that early-life associations in females were lost during the breeding season, but resurfaced during the subsequent wintering season. In males, the early-life associations persisted across both seasons. Association persistence was not mediated by genetic relatedness or familiarity. The high level of aggressiveness of males, but not females, in the breeding season suggests that males may have played a key role in shaping both their own social environment and that of their partners. We show that early-life social relationships can be maintained well into later life. Such relationships can be sustained even if they are temporarily disrupted, for example due to reproductive behaviour. Our findings therefore highlight that the early-life social environment can have life-long consequences on individuals’ social environment.
Model Based Inference of Large Scale Brain Networks with Approximate Bayesian Computation
Authors: West Timothy O. , Berthouze Luc , Farmer Simon F. , Cagnan Hayriye , Litvak Vladimir
Published: October 2019

Brain networks and the neural dynamics that unfold upon them are of great interest across the many scales of systems neuroscience. The tools of inverse modelling provide a way of both constraining and selecting models of large scale brain networks from empirical data. Such models have the potential to yield broad theoretical insights in the understanding of the physiological processes behind the integration and segregation of activity in the brain. In order to make inverse modelling computationally tractable, simplifying model assumptions have often been adopted that appeal to steady-state approximations to neural dynamics and thus prevent the investigation of stochastic or intermittent dynamics such as gamma or beta burst activity. In this work we describe a framework that uses the Approximate Bayesian Computation (ABC) algorithm for the inversion of neural models that can flexibly represent any statistical feature of empirically recorded data and eschew the need to assume a locally linearized system. Further, we demonstrate how Bayesian model comparison can be applied to fitted models to enable the selection of competing hypotheses regarding the causes of neural data. This work establishes a validation of the procedures by testing for both the face validity (i.e. the ability to identify the original model that has generated the observed data) and predictive validity (i.e. the consistency of the parameter estimation across multiple realizations of the same data). From the validation and example applications presented here we conclude that the proposed framework provides a novel opportunity to researchers aiming to explain how complex brain dynamics emerge from neural circuits.
DeepMicro: deep representation learning for disease prediction based on microbiome data
Authors: Oh Min , Zhang Liqing
Published: October 2019

Human microbiota plays a key role in human health and growing evidence supports the potential use of microbiome as a predictor of various diseases. However, the high-dimensionality of microbiome data, often in the order of hundreds of thousands, yet low sample sizes, poses great challenge for machine learning-based prediction algorithms. This imbalance induces the data to be highly sparse, preventing from learning a better prediction model. Also, there has been little work on deep learning applications to microbiome data with a rigorous evaluation scheme. To address these challenges, we propose DeepMicro, a deep representation learning framework allowing for an effective representation of microbiome profiles. DeepMicro successfully transforms high-dimensional microbiome data into a robust low-dimensional representation using various autoencoders and applies machine learning classification algorithms on the learned representation. In disease prediction, DeepMicro outperforms the current best approaches based on the strain-level marker profile in five different datasets. In addition, by significantly reducing the dimensionality of the marker profile, DeepMicro accelerates the model training and hyperparameter optimization procedure with 8X-30X speedup over the basic approach. DeepMicro is freely available at https://github.com/minoh0201/DeepMicro.
Migration of intestinal dendritic cell subsets upon intrinsic and extrinsic TLR3 stimulation
Authors: López Agnès Garcias , Bekiaris Vasileios , Luda Katarzyna Müller , Hütter Julia , Muleta Konjit Getachew , Nakawesi Joy , Ulmert Isabel , Kotarsky Knut , Malissen Bernard , O’Keeffe Meredith , Holzmann Bernhard , Agace William , Lahl Katharina
Published: October 2019

Initiation of adaptive immunity to particulate antigens in lymph nodes largely depends on their presentation by migratory dendritic cells (DCs). DC subsets differ in their capacity to induce specific types of immunity, allowing subset-specific DC-targeting to influence vaccination and therapy outcomes. Faithful drug design however requires exact understanding of subset-specific versus global activation mechanisms. cDC1, the subset of DCs that excel in supporting immunity towards viruses, intracellular bacteria and tumors, express uniquely high levels of the pattern recognition receptor TLR3. Using various genetic models, we show here that both the cDC1 and cDC2 subsets of cDCs are activated and migrate equally well in response to TLR3 stimulation in a cell extrinsic and TNFα dependent manner, but that cDC1 show a unique requirement for type I interferon signaling. Our findings reveal common and differing pathways regulating DC subset migration, offering important insights for the design of DC-based vaccination and therapy approaches.
First description of the sexual stage ofVenturia effusa, causal agent of pecan scab
Authors: Charlton Nikki D. , Yi Mihwa , Bock Clive H. , Zhang Minling , Young Carolyn A.
Published: October 2019

Venturia effusa, cause of pecan scab, is the most prevalent disease of pecan in the southeastern USA; epidemics of the disease regularly result in economic losses to the pecan industry. Recent characterization of the mating type distribution revealed the frequency of theMATidiomorphs are in equilibrium at various spatial scales, indicative of regular sexual recombination. However, the occurrence of the sexual stage ofV. effusahas never been observed, and the pathogen was previously believed to rely entirely on asexual reproduction. To explore the existence of a sexual cycle, we paired opposite mating types on oatmeal culture media. In initial experiments, cultures were incubated at 24 C for 2 mo for hyphal interactions to occur between mating types and then maintained at 4 C for 4 mo. Immature pseudothecia were initially observed but following exposure to a 12 h photoperiod for 2 weeks at 24 C, asci and ascospores developed. Further experiments explored the effect of time on pseudothecial development with 4 mo at 4 C as the optimal requirement. The results of this study demonstrate the heterothallic nature ofV. effusa.Following experiments investigated progeny from a sexual cross of an albino and a wild-type isolate. Evaluation of isolate pigmentation, mating type, and multilocus genotyping of single ascospore progeny provided evidence that recombination occurred within the sexual crosses. The impact of determining the source of the overwintering ascostroma will aid in management decisions to reduce the primary inoculum in the disease cycle.
Reward timing and its expression by inhibitory interneurons in the mouse primary visual cortex
Authors: Monk Kevin J , Allard Simon , Shuler Marshall G Hussain
Published: October 2019

Primary sensory cortex has historically been studied as a low-level feature detector, but has more recently been implicated in many higher-level cognitive functions. For instance, after an animal learns that a light predicts water at a fixed delay, neurons in primary visual cortex (V1) can produce “reward timing activity” (i.e., spike modulation of various forms that relate the interval between the visual stimulus and expected reward). The manner by which V1 produces these representations is unknown. Here, we combine behavior, in vivo electrophysiology, and optogenetics to investigate the characteristics of and circuit mechanisms underlying V1 reward timing in the head-fixed mouse. We find that reward timing activity is present in mouse V1, that inhibitory interneurons participate in reward timing, and that these representations are consistent with a theorized network architecture. Together, these results deepen our understanding of V1 reward timing and the manner by which it is produced.
Dietary xanthan gum alters antibiotic efficacy against the murine gut microbiota and attenuatesClostridioides difficilecolonization
Authors: Schnizlein Matthew K. , Vendrov Kimberly C. , Edwards Summer J. , Martens Eric C. , Young Vincent B.
Published: October 2019

Dietary fiber provides a variety of microbiota-mediated benefits ranging from anti-inflammatory metabolites to pathogen colonization resistance. A healthy gut microbiota protects againstClostridioides difficilecolonization. Manipulation of these microbes through diet may increase colonization resistance to improve clinical outcomes. The primary objective of this study was to identify how the dietary fiber xanthan gum affects the microbiota andC. difficilecolonization.

We added 5% xanthan gum to the diet of C57Bl/6 mice and examined its effect on the microbiota through 16S rRNA-gene amplicon sequencing and short-chain fatty acid analysis. Following either cefoperazone or an antibiotic cocktail administration, we challenged mice withC. difficileand measured colonization by monitoring colony-forming units.

Xanthan gum administration associates with increases in fiber degrading taxa and short-chain fatty acid concentrations. However, by maintaining both the diversity and absolute abundance of the microbiota during antibiotic treatment, the protective effects of xanthan gum administration on the microbiota were more prominent than the enrichment of these fiber degrading taxa. As a result, mice that were on the xanthan gum diet experienced limited to noC. difficilecolonization.

Xanthan gum administration alters mouse susceptibility toC. difficilecolonization by maintaining the microbiota during antibiotic treatment. While antibiotic-xanthan gum interactions are not well understood, xanthan gum has previously been used to bind drugs and alter their pharmacokinetics. Thus, xanthan gum may alter the activity of the oral antibiotics used to make the microbiota susceptible. Future research should further characterize how this and other common dietary fibers interact with drugs.

IMPORTANCE

A healthy gut bacterial community benefits the host by breaking down dietary nutrients and protecting against pathogens.Clostridioides difficilecapitalizes on the absence of this community to cause diarrhea and inflammation. Thus, a major clinical goal is to find ways to increase resistance toC. difficilecolonization by either supplementing with bacteria that promote resistance or a diet to enrich for those already present in the gut. In this study, we describe an interaction between xanthan gum, a human dietary additive, and the microbiota resulting in an altered gut environment that is protective againstC. difficilecolonization.
Predictive Representations in Hippocampal and Prefrontal Hierarchies
Authors: Brunec Iva K. , Momennejad Ida
Published: October 2019

As we navigate the world, we use learned representations of relational structures to explore and to reach goals. Studies of how relational knowledge enables inference and planning are typically conducted in controlled small-scale settings. It remains unclear, however, how people use stored knowledge in continuously unfolding navigation, e.g., walking long distances in a city. We hypothesized that multiscale predictive representations guide naturalistic navigation, and these scales are organized along posterior-anterior prefrontal and hippocampal hierarchies. We conducted model-based representational similarity analyses of neuroimaging data measured during navigation of realistically long paths in virtual reality. We tested the pattern similarity of each point–along each path–to a weighted sum of its successor points within predictive horizons of different scales. We found that anterior PFC showed the largest predictive horizons, posterior hippocampus the smallest, with the anterior hippocampus and orbitofrontal regions in between. Our findings offer novel insights into how cognitive maps support hierarchical planning at multiple scales.
Cover crops improve early season natural enemy recruitment and pest management in cotton production
Authors: Bowers Carson , Toews Michael , Liu Yangxuan , Schmidt Jason M.
Published: October 2019

A shift to more ecologically based farming practices would improve the sustainability and economic stability of agricultural systems. Habitat management in and around agricultural fields can provide stable environments that aid in the proliferation of natural enemy communities that moderate pest populations and injury. Winter cover crops offer a potentially cost-effective approach to improving habitat that supports natural enemy communities early in the growing season. We investigated the effects of winter cover crops including cereal rye (Secale cereal L.) and crimson clover (Trifolium incarnatum L.) on the abundance and diversity of natural enemies, key pest populations, biological control services, and cotton yield. Winter cover crops were established on 0.4 ha replicated field plots in the fall of 2017 and 2018. Suction sampling during each cotton development stage demonstrated that a rye cover crop promoted greater abundance and diversity of natural enemy communities in early cotton stages. Extensive leaf sampling of seedling cotton showed that cover crops significantly reduced thrips infestations. Furthermore, stink bug boll injury decreased on plots prepared with a rye cover compared to cotton lacking this additional habitat. Combining end of season yield results and management practices with an economic analysis of the costs of production, the value of cotton grown into a cover crop was cost competitive with conventional (no cover) cotton production. These results suggest that conventional growers utilizing cover crops could reduce insecticide inputs through natural reductions in pest pressure, and overall do not incur additional production costs.