bluuebunny/crossref_metadata_2025 huggingface dataset:
GenGraph: a python module for the simple generation and manipulation of genome graphs
Authors: Ambler Jon Mitchell , Mulaudzi Shandukani , Mulder Nicola
Published: October 2019

Background

As sequencing technology improves, the concept of a single reference genome is becoming increasingly restricting. In the case of Mycobacterium tuberculosis, one must often choose between using a genome that is closely related to the isolate, or one that is annotated in detail. One promising solution to this problem is through the graph based representation of collections of genomes as a single genome graph. Though there are currently a handful of tools that can create genome graphs and have demonstrated the advantages of this new paradigm, there still exists a need for flexible tools that can be used by researchers to overcome challenges in genomics studies.

Results

We present GenGraph, a Python toolkit and accompanying modules that use existing multiple sequence alignment tools to create genome graphs. Python is one of the most popular coding languages for the biological sciences, and by providing these tools, GenGraph makes it easier to experiment and develop new tools that utilise genome graphs. The conceptual model used is highly intuitive, and as much as possible the graph structure represents the biological relationship between the genomes. This design means that users will quickly be able to start creating genome graphs and using them in their own projects. We outline the methods used in the generation of the graphs, and give some examples of how the created graphs may be used. GenGraph utilises existing file formats and methods in the generation of these graphs, allowing graphs to be visualised and imported with widely used applications, including Cytoscape, R, and Java Script.

Conclusions

GenGraph provides a set of tools for generating graph based representations of sets of sequences with a simple conceptual model, written in the widely used coding language Python, and publicly available on Github.
Convergent evolution in toothed whale cochleae
Authors: Park Travis , Mennecart Bastien , Costeur Loïc , Grohé Camille , Cooper Natalie
Published: October 2019

Background

Odontocetes (toothed whales) are the most species-rich marine mammal lineage. The catalyst for their evolutionary success is echolocation - a form of biological sonar that uses high-frequency sound, produced in the forehead and ultimately detected by the cochlea. The ubiquity of echolocation in odontocetes across a wide range of physical and acoustic environments suggests that convergent evolution of cochlear shape is likely to have occurred. To test this, we used SURFACE; a method that fits Ornstein-Uhlenbeck (OU) models with stepwise AIC (Akaike Information Criterion) to identify convergent regimes on the odontocete phylogeny, and then tested whether convergence in these regimes was significantly greater than expected by chance.

Results

We identified three convergent regimes: (1) True’s (Mesoplodon mirus) and Cuvier’s (Ziphius cavirostris) beaked whales; (2) sperm whales (Physeter macrocephalus) and all other beaked whales sampled; and (3) pygmy (Kogia breviceps) and dwarf (Kogia sima) sperm whales and Dall’s porpoise (Phocoenoides dalli). Interestingly the ‘river dolphins’, a group notorious for their convergent morphologies and riverine ecologies, do not have convergent cochlear shapes. The first two regimes were significantly convergent, with habitat type and dive type significantly correlated with membership of the sperm whale + beaked whale regime.

Conclusions

The extreme acoustic environment of the deep ocean likely constrains cochlear shape, causing the cochlear morphology of sperm and beaked whales to converge. This study adds support for cochlear morphology being used to predict the ecology of extinct cetaceans.
7C: Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs
Authors: Ibn-Salem Jonas , Andrade-Navarro Miguel A.
Published: October 2019

Background

Knowledge of the three-dimensional structure of the genome is necessary to understand how gene expression is regulated. Recent experimental techniques such as Hi-C or ChIA-PET measure long-range chromatin interactions genome-wide but are experimentally elaborate, have limited resolution and such data is only available for a limited number of cell types and tissues.

Results

While ChIP-seq was not designed to detect chromatin interactions, the formaldehyde treatment in the ChIP-seq protocol cross-links proteins with each other and with DNA. Consequently, also regions that are not directly bound by the targeted TF but interact with the binding site via chromatin looping are co-immunoprecipitated and sequenced. This produces minor ChIP-seq signals at loop anchor regions close to the directly bound site. We use the position and shape of ChIP-seq signals around CTCF motif pairs to predict whether they interact or not. We implemented this approach in a prediction method, termed Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs (7C). We applied 7C to all CTCF motif pairs within 1 Mb in the human genome and validated predicted interactions with high-resolution Hi-C and ChIA-PET. A single ChIP-seq experiment from known architectural proteins (CTCF, Rad21, Znf143) but also from other TFs (like TRIM22 or RUNX3) predicts loops accurately. Importantly, 7C predicts loops in cell types and for TF ChIP-seq datasets not used in training.

Conclusion

7C predicts chromatin loops which can help to associate TF binding sites to regulated genes. Furthermore, profiling of hundreds of ChIP-seq datasets results in novel candidate factors functionally involved in chromatin looping. Our method is available as an R/Bioconductor package: http://bioconductor.org/packages/sevenC.
RNA-Seq based transcriptome analysis during bovine viral diarrhoea virus (BVDV) infection
Authors: Liu Cun , Liu Yanhan , Liang Lin , Cui Shangjin , Zhang Yanming
Published: October 2019

Background

Bovine viral diarrhoea virus (BVDV) is the member of the genus Pestivirus within the Flaviviridae family and responsible for severe economic losses in the cattle industry. BVDV can employ ‘infect-and-persist’ strategy and ‘hit-and-run’ strategy to remain associated with hosts and thus contributes to BVDV circulation in cattle herds. BVDV have also evolved various strategies to evade the innate immunity of host. To further understand the mechanisms by which BVDV overcomes the host cell innate immune response and provide more clues for further understanding the BVDV-host interaction, in this descriptive study, we conducted a investigation of differentially expressed genes (DEGs) of the host during BVDV infection by RNA-Seq analysis.

Results

Our analysis identified 1297, 1732, 3072, and 1877 DEGs in the comparison groups mock vs. MDBK cells infected with BVDV post 2 h (MBV2h), mock vs. MBV6h, mock vs. MBV12h, and mock vs. MBV24h, respectively. The reproducibility and repeatability of the results were validated by RT-qPCR. Enrichment analyses of GO annotations and KEGG pathways revealed the host DEGs that are potentially induced by BVDV infection and may participate in BVDV-host interactions. Protein-protein interaction (PPI) network analyses identified the potential interactions among the DEGs. Our findings suggested that BVDV infection induced the upregulation of genes involved in lipid metabolism. The expression of genes that have antiviral roles, including ISG15, Mx1, OSA1Y, were found to be downregulated and are thus potentially associated with the inhibition of host innate immune system during BVDV infection. The expression levels of F3, C1R, KNG1, CLU, C3, FB, SERPINA5, SERPINE1, C1S, F2RL2, and C2, which belong to the complement and coagulation signalling cascades, were downregulated during BVDV infection, which suggested that the complement system might play a crucial role during BVDV infection.

Conclusion

In this descriptive study, our findings revealed the changes in the host transcriptome expression profile during BVDV infection and suggested that BVDV-infection induced altering the host’s metabolic network, the inhibition of the expression of antiviral proteins and genes within the complement system might be contributed to BVDV proliferation. The above findings provided unique insights for further studies on the mechanisms underlying BVDV-host interactions.
Water-deficit responsive microRNAs in the primary root growth zone of maize
Authors: Seeve Candace M. , Sunkar Ramanjulu , Zheng Yun , Liu Li , Liu Zhijie , McMullen Michael , Nelson Sven , Sharp Robert E. , Oliver Melvin J.
Published: October 2019

Background

MicroRNA-mediated gene regulatory networks play a significant role in plant growth and development and environmental stress responses.

Results

We identified 79 microRNAs (miRNAs) and multiple miRNA variants (isomiRs) belonging to 26 miRNA families in the primary root growth zone of maize seedlings grown at one of three water potentials: well-watered (− 0.02 MPa), mild water deficit stress (− 0.3 MPa), and severe water deficit stress (− 1.6 MPa). The abundances of 3 miRNAs (mild stress) and 34 miRNAs representing 17 families (severe stress) were significantly different in water-deficit stressed relative to well-watered controls (FDR < 0.05 and validated by stem loop RT-qPCR). Degradome sequencing revealed 213 miRNA-regulated transcripts and trancriptome profiling revealed that the abundance of 77 (miRNA-regulated) were regulated by water-defecit stress. miR399e,i,j-3p was strongly regulated by water-defcit stress implicating the possibility of nutrient deficiency during stress.

Conclusions

We have identified a number of maize miRNAs that respond to specific water deficits applied to the primary root growth zone. We have also identified transcripts that are targets for miRNA regulation in the root growth zone under water-deficit stress. The miR399e,i,j-3p that is known to regulate phosphate uptake in response to nutrient deficiencies responds to water-deficit stress, however, at the seedling stage the seed provides adequate nutrients for root growth thus miR399e,i,j-3p may play a separate role in water-deficit responses. A water-deficit regulated maize transcript, similar to known miR399 target mimics, was identified and we hypothesized that it is another regulatory player, moderating the role of miR399e,i,j-3p, in primary root growth zone water deficit responses.
Fluctuations in Fabaceae mitochondrial genome size and content are both ancient and recent
Authors: Choi In-Su , Schwarz Erika N. , Ruhlman Tracey A. , Khiyami Mohammad A. , Sabir Jamal S. M. , Hajarah Nahid H. , Sabir Mernan J. , Rabah Samar O. , Jansen Robert K.
Published: October 2019

Background

Organelle genome studies of Fabaceae, an economically and ecologically important plant family, have been biased towards the plastid genome (plastome). Thus far, less than 15 mitochondrial genome (mitogenome) sequences of Fabaceae have been published, all but four of which belong to the subfamily Papilionoideae, limiting the understanding of size variation and content across the family. To address this, four mitogenomes were sequenced and assembled from three different subfamilies (Cercidoideae, Detarioideae and Caesalpinioideae).

Results

Phylogenetic analysis based on shared mitochondrial protein coding regions produced a fully resolved and well-supported phylogeny that was completely congruent with the plastome tree. Comparative analyses suggest that two kinds of mitogenome expansions have occurred in Fabaceae. Size expansion of four genera (Tamarindus,Libidibia,Haematoxylum, andLeucaena) in two subfamilies (Detarioideae and Caesalpinioideae) occurred in relatively deep nodes, and was mainly caused by intercellular gene transfer and/or interspecific horizontal gene transfer (HGT). The second, more recent expansion occurred in the Papilionoideae as a result of duplication of native mitochondrial sequences. Family-wide gene content analysis revealed 11 gene losses, four (rps2,7,11and13) of which occurred in the ancestor of Fabaceae. Losses of the remaining seven genes (cox2,rpl2,rpl10,rps1,rps19,sdh3,sdh4) were restricted to specific lineages or occurred independently in different clades. Introns of three genes (cox2,ccmFcandrps10) showed extensive lineage-specific length variation due to large sequence insertions and deletions. Shared DNA analysis among Fabaceae mitogenomes demonstrated a substantial decay of intergenic spacers and provided further insight into HGT between the mimosoid clade of Caesalpinioideae and the holoparasiticLophophytum(Balanophoraceae).

Conclusion

This study represents the most exhaustive analysis of Fabaceae mitogenomes so far, and extends the understanding the dynamic variation in size and gene/intron content. The four newly sequenced mitogenomes reported here expands the phylogenetic coverage to four subfamilies. The family has experienced multiple mitogenome size fluctuations in both ancient and recent times. The causes of these size variations are distinct in different lineages. Fabaceae mitogenomes experienced extensive size fluctuation by recruitment of exogenous DNA and duplication of native mitochondrial DNA.
Potential use of a diluted high-relaxivity gadolinium-based intra-articular contrast agent for magnetic resonance arthrography: an in-vitro study
Authors: Messina Carmelo , Albano Domenico , Orlandi Davide , Chianca Vito , Corazza Angelo , Ferrari Federica , Gitto Salvatore , Sconfienza Luca Maria
Published: October 2019

Background

Magnetic resonance arthrography (MRA) requires intra-articular injection of gadolinium-based diluted paramagnetic contrast material. To our knowledge, gadobenate dimeglumine (Gd-BOPTA) has never been used for intra-articular applications. Our aim was to test in vitro different concentrations of Gd-BOPTA to be potentially used to perform MRA.

Methods

Gd-BOPTA was diluted in saline (NaCl 0.9%) to achieve different concentrations (4 mmol/l; 2 mmol/l; 1 mmol/l; 0.67 mmol/l; 0.5 mmol/l). Six sets of five sterile pipes were prepared with 5 ml of each solution, five sets added with 0.5 ml of fresh synovial fluid. Two separate pipes were prepared with 5 ml of gadopentetate dimeglumine (Gd-DTPA) at 2 mmol/l, one pipe added with 0.5 ml of synovial fluid. Pipes were imaged using a T1-weighted sequence at 1.5 T. For each pipe, signal intensity (SI) in arbitrary units (au) was measured.

Results

SI reproducibility range was 86–99%. Mean Gd-BOPTA SI in pipes containing synovial fluid increased from 1236 ± 8au (0.5 mmol/l) up to 1610 ± 44au (1 mmol/l) and down to 1405 ± 33au (4 mmol/l). Mean Gd-BOPTA SI in pipes without synovial fluid increased from 1184 ± 29au (0.5 mmol/l) up to 1530 ± 38au (1 mmol/l), and down to 1347 ± 39au (4 mmol/l). SI of pipes without synovial fluid was lower than that of pipes with synovial fluid for both Gd-BOPTA and Gd-DTPA (P ≤ 0.002). Regarding pipes with synovial fluid, mean Gd-DTPA SI at 2 mmol/l was 1246 ± 27au. Compared with Gd-BOPTA, SI was not different at 0.5 mmol/l (− 0.2%, P = 0.587) while it was higher (P < 0.001) at all other concentrations (range + 13.3%[4 mmol/l] − + 28.3%[1 mmol/l]). Regarding pipes without synovial fluid, mean Gd-DTPA SI at 2 mmol/l was 1275 ± 56au. Compared with Gd-BOPTA, SI was lower at 0.5 mmol/l (− 6.8%,P < 0.001), while it was higher (P < 0.001) at all other concentrations (range + 6.1%[4 mmol/l] − + 19.6% [1 mmol/l]).

Conclusions

In vitro, Gd-BOPTA at 1 mmol/ had a + 28% SI increase in comparison to Gd-DTPA 2 mmol/l. SI similar to Gd-DTPA can be obtained using one fourth concentration of Gd-BOPTA.
The diffuse involvement of anti-N-methyl-D-aspartate receptor encephalitis in brain: a case report
Authors: Jiang Yun , Ma Jianpeng , Gong Tao , Hao Hongjun , Chen Haibo
Published: October 2019

Background

Anti-N-methyl-D-aspartate receptor (NMDAR) encephalitis is a severe and most common autoimmune encephalitis in patients under 40 years old. Anti-NMDAR encephalitis has various clinical and neuroimaging findings. Here we report a special case of an anti-NMDAR encephalitis who had diffuse lesions in bilateral hemispheres with mild mass effects in left basal ganglia area.

Case presentations

A 28-year-old female anti-NMDAR encephalitis patient mainly presented with headache and fever. Brain magnetic resonance image (MRI) showed slightly contrasted diffuse lesions, involving the left temporal and frontal lobes, left basal ganglia area and splenium of corpus callosum, as well as the right frontal lobe, with mild edema surrounded in the left basal ganglia area. Cerebrospinal fluid (CSF) revealed a moderate pleocytosis with normal protein and glucose levels. Anti-NMDAR antibodies were identified in CSF. Transvaginal ovarian ultrasound did not reveal an ovarian teratoma. The patient was treated with immunoglobulin and steroid, and had a good recovery.

Conclusions

Anti-NMDAR encephalitis has no special clinical manifestations and brain MRI is highly variable, which could be unremarkable or abnormal involving white and grey matters. The extensive lesions in frontal and temporal lobes, and basal ganglia area, with mild mass effects, have not been described previously. Recognition of various changes in brain MRI will enable the early detection of anti-NMDAR antibody and then effective treatments.
Revisiting: “A pre-post study of a multi-country scale up of resuscitation training of facility birth attendants: does helping babies breathe training save lives?”
Authors: Berkelhamer Sara , Singhal Nalini
Published: October 2019

Background

Helping Babies Breathe (HBB) is a low cost, skills-based neonatal resuscitation education program designed specifically for use in low resource settings. Studies from Tanzania, India and Nepal have demonstrated that HBB training results in decreased rates of fresh still birth and/or neonatal mortality. However, less is known regarding the impact of training on neonatal mortality at a population level. Bellad et al. utilized (BMC Pregnancy Childbirth. 2016;16 (1):222) utilized population based registries to evaluate outcomes before and after training of facility birth attendants. Their study entitled “A pre-post study of a multi-country scale up of resuscitation training of facility birth attendants: Does Helping Babies Breathe training save lives?” suggested facility based training was not associated with consistent improvements in neonatal mortality on a population level.

Discussion

Combining outcomes from three diverse settings may have under-estimated the impact of HBB training. We remain concerned that the modest benefits observed in the Kenyan site were lost with compiling of data.

The statement that HBB “was not associated with consistent improvements in mortality” may lead to the mistaken conclusion that improvements in neonatal mortality were not seen, when in fact, they were in selected cohorts. With numerous studies demonstrating potential for reduced neonatal mortality as a result of HBB training, we encourage interpretation of these findings in the context of local care.
Effects of sanitation practices on adverse pregnancy outcomes in India: a conducive finding from recent Indian demographic health survey
Authors: Patel Ratna , Gupta Ajay , Chauhan Shekhar , Bansod Dhananjay W.
Published: October 2019

Background

Several risk factors predisposing women and their live-borns to adverse outcomes during pregnancy have been documented. Little is known about sanitation being a factor contributing to adverse pregnancy outcomes in India. The role of sanitation in adverse pregnancy outcomes remains largely unexplored in the Indian context. This study is an attempt to bring the focus on sanitation as a factor in adverse pregnancy outcome. Along with the sanitation factors, few confounder variables have also been studied in order to understand the adverse pregnancy outcomes.

Methods

The study is based on the fourth round of National Family Health Survey (NFHS-IV) covering 26,972 married women in the age-group 15–49. The study variables include the mother’s age, Body Mass Index (BMI), education, anemia, and Antenatal care (ANC) visits during their last pregnancy. The household level variable includes place of residence, religion, caste, wealth index, access to toilet, type of toilet, availability of water within toilet premises, and facility of hand wash near the toilet. Children study variables include Low Birth Weight (LBW), the order of birth (Parity), and the death of the children of the women in the last 5 years. The target variable Adverse Pregnancy Outcome (APO) was constructed using children born with low birth weight or died during the last pregnancy.

Results

We calculated both adjusted as well as unadjusted odds ratios for a better understanding of the association between sanitation and adverse pregnancy outcomes. Findings from the study showed that women who did not have access to a toilet within the house had a higher risk of adverse pregnancy outcome. In the multivariable model, no association was observed for adverse pregnancy outcome among women who did not have access to toilet and women who used shared toilet. Teenage (15–19 years), uneducated, underweight and anemic mothers were more likely to face APO as compare to other mothers in similar characteristics group.

Conclusions

Our findings contribute to the decidedly less available literature on maternal sanitation behaviour and adverse pregnancy outcomes. Our results support that sanitation is a very significant aspect for women who are about to deliver a baby as there was an association between sanitation and adverse pregnancy outcome. Education on sanitation practices is the need of the hour as much as it needs to follow.
Confirmatory trial of non-amputative digit preservation surgery for subungual melanoma: Japan Clinical Oncology Group study (JCOG1602, J-NAIL study protocol)
Authors:   on behalf of the Dermatologic Oncology Group of the Japan Clinical Oncology Group, Tanaka Kiyo , Nakamura Yasuhiro , Mizutani Tomonori , Shibata Taro , Tsutsumida Arata , Fukuda Haruhiko , Matsushita Shigeto , Aoki Megumi , Namikawa Kenjiro , Ohe Shuichi , Fukushima Satoshi , Yamazaki Naoya
Published: October 2019

Background

Amputation is the standard of care even for early-stage subungual melanomas (SUMs), known as nail apparatus melanoma, because the nail bed and nail matrix are close to the distal phalanx. However, a recent study demonstrated that not all patients with SUMs had histologic invasion of the underlying distal phalanx. As most SUMs occur in the thumb or big toe, amputation of either the thumb or big toe substantially interferes with activities of daily living, including poor cosmesis, loss of function, and phantom pain. Non-amputative digit preservation surgery can thus be applied in such cases without compromising patient prognosis.

Methods

We are conducting a multi-institutional single-arm trial to confirm the safety and efficacy of non-amputative digit preservation surgery. We will compare our results with those reported in the Japanese Melanoma Study, in which patients underwent amputation for SUMs as a traditional standard of care. Patients aged between 20 and 80 years with stage I, II, or III without evidence of tumor invasion to the underlying distal phalanx on preoperative radiograph are included in the study. The primary endpoint is major relapse-free survival (major RFS), which does not include local recurrence as an event; secondary endpoints include overall survival, digit-preservation survival, relapse-free survival, local relapse-free survival, partial relapse-free survival, and incidence of adverse events. A total of 85 patients from 21 Japanese institutions will be recruited within 5.5 years, and the follow-up period will last at least 5 years. The Japan Clinical Oncology Group Protocol Review Committee approved this study protocol in August 2017, and patient enrollment began in November 2017. Ethical approval was obtained from each institution’s Institutional Review Board prior to patient enrollment.

Discussion

This is the first prospective trial to confirm the safety and efficacy of non-amputative digit preservation surgery for SUM without distant metastasis or bony invasion. The results of this trial could provide evidence to support this less-invasive surgery as a new standard of care to preserve adequately functioning digits.

Trial registration

Registry number: UMIN000029997. Date of Registration: 16/Nov/2017. Date of First Participant Enrollment: 12/Dec/2017.
Prevalence and associated factors of neurodevelopmental disability among infants in eastern Uganda: a population based study
Authors: Namazzi Gertrude , Hildenwall Helena , Mubiri Paul , Hanson Claudia , Nalwadda Christine , Nampijja Margaret , Kakooza-Mwesige Angelina , Waiswa Peter , Tumwine James K.
Published: October 2019

Background

Neurodevelopmental disability (NDD) is increasingly acknowledged as one of the important causes of disease burden in low income countries. None the less, there is a dearth of data on the burden of NDD and its determinants in these settings. We aimed to establish the prevalence and factors associated with NDD among infants in Eastern Uganda.

Methods

We assessed 487 infants aged 9–12 months within Iganga-Mayuge Health Demographic Surveillance Site in Eastern Uganda using the Malawi Developmental Assessment Tool. The tool has four domains: gross motor, fine motor, language and social domains. An infant failed a domain if she/he failed more than two parameters of the expected at his/her age.

We interviewed mothers on factors that could influence the infants’ neurodevelopmental outcomes. Data were analysed using STATA version 14. We used odds ratios and 95% confidence intervals to assess statistical significance of associations.

Results

Of the 487 infants, 62(12.7%) had an NDD in at least one of the domains. The most affected was social behaviour where 52(10.7%) infants had an NDD. Severe impairment was seen among 9(1.8%) infants with NDD in either three or four domains.

Factors associated with NDD at multivariate logistic regression included: parity of more than three children (aOR = 1.8, 95% CI: 1.02–3.18); failure to cry at birth (aOR = 3.6, 95% CI: 1.46–9.17) and post-neonatal complications (aOR = 4.15, 95% CI: 1.22–14.10). Low birth weight, immediate and exclusive breast feeding were not significantly associated with NDD.

Conclusion

We found a high NDD burden among infants particularly in the social behaviour domain. To optimise the socio-neural development of infants, programs are needed to educate and work with families on how to engage and stimulate infants. Existing immunisation clinics and community health worker strategies provide an excellent opportunity for stemming this burden.
Does your neighborhood protect you from being depressed? A study on social trust and depression in Indonesia
Authors: Fahmi Mohamad , Panjaitan Nur Afni , Habibie Ibnu , Siregar Adiatma Y. M. , Amarullah Gilang , Rahma  , Sunjaya Deni K.
Published: October 2019

Background

Prevalence of depression in Indonesia is estimated at about 3.7% of the total population, although the actual may be higher. Studies worldwide have linked the environment where people live to their mental health status. However, little research is found in Indonesia regarding this link. We examined the association between individuals’ perception towards their neighborhood and their depression symptoms.

Methods

Social trust was measured at the individual (level 1) and community (level 2) levels based on the Indonesian Family Life Survey 5 (IFLS5) in 2014. Depression was measured using the 10-item Center for Epidemiologic Studies-Depression Scale Revised (CESD-R-10) and the scores were transformed into logit form using the Rasch model. Multilevel regression was used to determine correlations.

Results

Of the total sample of 14,227 respondents in this study, about 19.4% had experienced severe depression symptoms in the past week. Social trust was found to be significantly associated with severe depression symptoms. The weaker the individuals’ social trust towards their neighbourhood, the higher the probability of experiencing severe depression symptoms would be.

Conclusions

This study shows that social trust is associated with the severity of depression symptoms: the higher the social trust, the lower the probability of having severe depression symptoms is. Depression symptoms may also be attributed to significant differences between communities.
The effect of job aids on knowledge retention among Patent and Proprietary Medicine Vendors trained to administer injectable contraceptives: longitudinal results from implementation science in Nigeria
Authors: Chace Dwyer Sara , Jain Aparna , Ishaku Salisu Mohammed , Okunade Faizah Tosin , Uzomba Chiamaka , Adebayo Adedamola , Tobey Elizabeth
Published: October 2019

Background

To increase access to voluntary family planning (FP) services, Nigerian policymakers are debating how to task share injectable contraceptive services to drug shop owners known as Patent and Proprietary Medicine Vendors (PPMVs). Task sharing FP services to drug shops is a promising practice, but information is needed on how to ensure high quality FP services. This analysis assesses the effects of job aids on PPMVs’ knowledge of injectable contraceptives 9 months after receiving a standardized training.

Methods

One hundred ninety-four PPMVs were trained on FP counseling and administration of injectable contraceptives in Bauchi, Cross River, Ebonyi and Kaduna states. PPMVs were interviewed before, after, and 9 months after the training. Three variables were used to assess injectable contraceptive knowledge: 1) intramuscular depot-medroxyprogesterone acetate (DMPA-IM) knowledge: a combination of three questions related to device type, injection location, and reinjection frequency; 2) subcutaneous DMPA (DMPA-SC) knowledge: a combination of the same three questions but for DMPA-SC; and 3) knowledge of at least 4 of the 7 common injectable side effects. Three separate adjusted logistic regression models were conducted to determine the factors that influence PPMV knowledge of injectable contraceptives 9 months after the training.

Results

Over half of PPMVs (56%) reported using at least two job aids at 9 months. PPMVs’ knowledge of DMPA-IM, DMPA-SC and side effects were low before the training but increased immediately after. Nine months later, knowledge remained higher than pre-test levels but generally reduced compared to posttest levels. PPMVs who reported using at least two FP job aids were 2.6 (95% CI: 1.4–5.1) times more likely to have DMPA-IM knowledge 9 months after the training compared to those who used one or no job aids, while adjusting for PPMV characteristics. Similar results were observed for knowledge of DMPA-SC (AOR: 2.5; 95% CI: 1.2–4.6) and side effects (AOR: 2.5; 95% CI: 1.3–4.8).

Conclusion

PPMVs who used at least two FP job aids were more likely to correctly answer key injectable contraceptive questions 9 months after training. Incorporating proven job aids into routine trainings is a low-cost strategy that can reinforce knowledge and help PPMVs to retain information.
What’s for lunch? The content and quality of lunches consumed by Dutch primary schoolchildren and the differences between lunches consumed at home and at school
Authors: Rongen Frédérique C. , van Kleef Ellen , Sanjaya Sienna , Vingerhoeds Monique H. , Buurma-Rethans Elly J. M. , van den Bogaard Coline , van Rossum Caroline T. M. , Seidell Jacob C. , Dijkstra S. Coosje
Published: October 2019

Background

Lunch is an important part of a healthy diet, which is essential for the development, growth and academic performance of school-aged children. Currently there is an increasing number of Dutch primary schoolchildren who are transitioning from eating lunch at home to school. There is limited knowledge about the current quality of the lunches consumed by primary schoolchildren in the Netherlands and whether there are any differences between lunches consumed at home or at school. To investigate differences in content and quality of lunches consumed by Dutch primary schoolchildren at home and at school.

Methods

Cross-sectional study among 363 Dutch primary schoolchildren aged 4–12 years based on the first two years of the 2012–2016 Dutch National Food Consumption Survey. Demographic characteristics were obtained through a questionnaire. Diet was assessed with two non-consecutive 24-h dietary recalls. Quality of lunches was assessed on their nutritional quality whether they fitted the nutritional guidelines. ‘Nonparametric tests were used to examine the content and quality of the lunches between place of consumption and parental educational position.

Results

The most consumed lunch products among primary schoolchildren were bread, dairy products and sugar-sweetened beverages. Fruit and vegetable consumption was very low. Consumption of milk and other dairy products was higher among children who eat lunch at home than children who eat lunch at school (p < 0.01). Consumption of sugar-sweetened beverages was higher among children who eat lunch at school than children who eat lunch at home (p < 0.01), and at school a higher proportion of the drinks did not fit within the Dutch dietary recommendations (p < 0.01).

Conclusions

The current content of the lunches consumed by Dutch primary schoolchildren leaves room for improvement, especially regarding fruit and vegetables. The statistically significantly higher consumption of sugar-sweetened beverages and lower consumption of milk and dairy products at school vs. home is worrisome, as currently more children in the Netherlands are transitioning to having lunch at school.
Comparison of glenohumeral joint rotation between asymptomatic subjects and patients with subacromial impingement syndrome using cine-magnetic resonance imaging: a cross-sectional study
Authors: Kenmoku Tomonori , Matsuki Keisuke , Ochiai Nobuyasu , Sonoda Masaru , Ishida Takumi , Sasaki Shuichi , Tanaka Yuji , Nakawaki Mitsufumi , Nagura Naoshige , Tazawa Ryo , Sasaki Yu , Banks Scott A. , Takaso Masashi
Published: October 2019

Background

The purpose of this study to compare glenohumeral joint motion during active shoulder axial rotation between subacromial impingement syndrome (SIS) shoulders and asymptomatic shoulders using cine-magnetic resonance imaging (cine-MRI). Measurement of glenohumeral joint motion via manual intervention does not assess the usual glenohumeral joint motion, and the glenoid surface cannot be confirmed manually. However, cine-MRI can produce clear images of glenohumeral joint rotation. Therefore, we sought to measure the active ROM of the glenohumeral rotation using cine-MRI.

Methods

Seventy-three shoulders in 42 asymptomatic volunteers and 110 SIS shoulders in 103 consecutive patients were included in this study. We evaluated 36 matched pairs (72 shoulders in total) adjusting for baseline characteristics with propensity score matching method. The patients underwent cine-MRI during axial rotation of the adducted arm. During imaging, participants rotated their shoulder from the maximum internal rotation to the maximum external rotation over the first 10 s and then back to the maximum internal rotation over the subsequent 10 s. We assessed internal/external rotation, and compared the asymptomatic and SIS shoulders in this regard. Evaluation of rotation angles was performed on a series of axial images through the humeral head center.

Results

The mean internal rotation angles of the asymptomatic and patient groups were 55° ± 10° and 41° ± 23°, respectively, (P = .002; 95% Confidence Interval [CI], 51–58 vs 33–49); the mean external rotation angles were 47° ± 15° and 21° ± 25°, respectively, (P < .001; CI, 42–52 vs 13–29).

Conclusions

Compared to asymptomatic shoulders, SIS shoulders showed significantly restricted glenohumeral rotation as determined by cine-MRI. Our results suggested that the significant limitation of active glenohumeral rotation might be associated with rotator cuff dysfunction.
Effects of pre-surgery physiotherapy on walking ability and lower extremity strength in patients with degenerative lumbar spine disorder: Secondary outcomes of the PREPARE randomised controlled trial
Authors: Fors Maria , Enthoven Paul , Abbott Allan , Öberg Birgitta
Published: October 2019

Background

Degenerative lumbar spine disorders are common among musculoskeletal disorders. When disabling pain and radiculopathy persists after adequate course of rehabilitation and imaging confirms compressive pathology, surgical decompression is indicated. Prehabilitation aiming to augment functional capacity pre-surgery may improve physical function and activity levels pre and post-surgery. This study aims to evaluate the effect and dose-response of pre-surgery physiotherapy on quadriceps femoris strength and walking ability in patients with degenerative lumbar spine disorders compared to waiting-list controls and their association with postoperative physical activity level.

Method

In this single blinded, 2-arm randomised controlled trial, 197 patients were consecutively recruited. Inclusion criteria were: MRI confirmed diagnosis and scheduled for surgery due to disc herniation, lumbar spinal stenosis, degenerative disc disease or spondylolisthesis, ages 25-80 years. Patients were randomised to 9 weeks of pre-surgery physiotherapy or to waiting-list. Patient reported physical activity level, walking ability according to Oswestry Disability Index item 4, walking distance according to the SWESPINE national register and physical outcome measures including the timed ten-meter walk test, maximum voluntary isometric quadriceps femoris muscle strength, patient-rated were collected at baseline and follow-up. Parametric or non-parametric within and between group comparisons as well as multivariate regression was performed.

Results

Patients who received pre-surgery physiotherapy significantly improved in all variables from baseline to follow-up (p < 0.001 – p < 0.05) and in comparison to waiting-list controls (p < 0.001 – p < 0.028). Patients adhering to ≥12 treatment sessions significantly improved in all variables (p < 0.001 – p < 0.032) and those receiving 0-11 treatment session in only normal walking speed (p0.035) but there were no significant differences when comparing dosages. Physical outcome measures after pre-surgery physiotherapy together significantly explain 27.5% of the variation in physical activity level 1 year after surgery with pre-surgery physical activity level having a significant multivariate association.

Conclusion

Pre-surgery physiotherapy increased walking ability and lower extremity strength in patients with degenerative lumbar spine disorders compared to waiting-list controls. A clear treatment dose-response response relationship was not found. These results implicate that pre-surgery physiotherapy can influence functional capacity before surgical treatment and has moderate associations with maintained postoperative physical activity levels mostly explained by physical activity level pre-surgery.

Trial registration

NCT02454400. Trial registration date: August 31st 2015, retrospectively registered.
Effect of lordosis on adjacent levels after lumbar interbody fusion, before and after removal of the spinal fixator: a finite element analysis
Authors: Tsuang Fon-Yih , Tsai Jui-Chang , Lai Dar-Ming
Published: October 2019

Background

Literature indicates that adjacent-segment diseases after posterior lumbar interbody fusion with pedicle screw fixation accelerate degenerative changes at unfused adjacent segments due to the increased motion and intervertebral stress. Sagittal alignment of the spine is an important consideration as achieving proper lordosis could improve the outcome of spinal fusion and avoid the risk of adjacent segment diseases. Therefore, restoration of adequate lumbar lordosis is considered as a major factor in the long-term success of lumbar fusion. This study hypothesized that the removal of internal fixation devices in segments that have already fused together could reduce stress at the disc at adjacent segments, particularly in patients with inadequate lordosis. The purpose of this study was to analyze the biomechanical characteristics of a single fusion model (posterior lumbar interbody fusion with internal fixation) with different lordosis angles before and after removal of the internal fixation device.

Methods

Five finite element models were constructed for analysis; 1) Intact lumbar spine without any implants (INT), 2) Lumbar spine implanted with a spinal fixator and lordotic intervertebral cage at L4-L5 (FUS-f-5c), 3) Lumbar spine after removal of the spinal fixator (FUS-5c), 4) Lumbar spine implanted with a spinal fixator and non-lordotic intervertebral cage at L4-L5 (FUS-f-0c), and 5) Lumbar spine after removal of the spinal fixator from the FUS-f-0c model (FUS-0c).

Results

The ROM of adjacent segments in the FUS-f-0c model was found to be greater than in the FUS-f-5c model. After removing the fixator, the adjacent segments in the FUS-5c and FUS-0c models had a ROM that was similar to the intact spine under all loading conditions. Removing the fixator also reduced the contact forces on adjacent facet joints and reduced the peak stresses on the discs at adjacent levels. The greatest increase in stress on the discs was found in the FUS-f-0c model (at both L2/L3 and L3/L4), with intervertebral stress at L3/L4 increasing by 83% when placed in flexion.

Conclusions

This study demonstrated how removing the spinal fixation construct after bone fusion could reduce intradiscal pressure and facet contact forces at adjacent segments, while retaining a suitable level of lumbar lordosis.
Association between plasma adipsin level and mild cognitive impairment in Chinese patients with type 2 diabetes: a cross-sectional study
Authors: Guo Dan , Yuan Yang , Huang Rong , Tian Sai , Wang Jiaqi , Lin Hongyan , An Ke , Han Jin , Wang Shaohua
Published: October 2019

Background

The adipokine adipsin contributes to insulin resistance (IR), inflammation, and obesity, which are all regarded as high-risk factors for mild cognitive impairment (MCI) in patients with type 2 diabetes mellitus. This research aimed to uncover the role of adipsin in Chinese type 2 diabetes mellitus (T2DM) population with early cognitive dysfunction and determine whether adipsin contributes to diabetic MCI caused by IR.

Methods

In our study, 126 patients with T2DM were enrolled. The Montreal Cognitive Assessment (MoCA) was used to assess cognitive impairment. Demographic data and neuropsychological test results were evaluated. Plasma adipsin level was measured by enzyme-linked immunosorbent assay.

Results

The MCI group (n = 57) presented higher plasma adipsin levels compared with the healthy controls (p = 0.018). After adjustment for educational attainment, and age, begative correlations were found between plasma adipsin levels and MoCA, Mini Mental State Exam, and Verbal Fluency Test scores(r = − 0.640, p < 0.001; r = − 0.612, p < 0.001; r = − 0.288, p = 0.035; respectively). Correlation analysis demonstrated that adipsin levels were significantly positively correlated with fasting C-peptide; homeostasis model of assessment for insulin resistance (HOMA-IR) (r = 0.368, p < 0.001; r = 0.494, p < 0.001; respectively). Multivariable regression analysis further indicated that high plasma adipsin level was a significant independent determinant of MCI in the Chinese population withT2DM (p = 0.017).

Conclusions

Elevated plasma adipsin level was associated with MCI in Chinese T2DM patients. Further large-scale studies should be designed to determine whether adipsin is linked to IR-associated susceptibility to early cognitive decline in T2DM patients.
Context, mechanisms and outcomes in end-of-life care for people with advanced dementia: family carers perspective
Authors: Kupeli Nuriye , Sampson Elizabeth L. , Leavey Gerard , Harrington Jane , Davis Sarah , Candy Bridget , King Michael , Nazareth Irwin , Jones Louise , Moore Kirsten
Published: October 2019

Background

Keeping people living with advanced dementia in their usual place of residence is becoming a key governmental goal but to achieve this, family carers and health care professionals must negotiate how to provide optimal care. Previously, we reported a realist analysis of the health care professional perspective. Here, we report on family carer perspectives. We aimed to understand the similarities and differences between the two perspectives, gain insights into how the interdependent roles of family carers and HCPs can be optimised, and make recommendations for policy and practice.

Method

Qualitative study using a realist approach in which we used the criteria from guidance on optimal palliative care in advanced dementia to examine key contexts, mechanisms and outcomes highlighted by family carers.

Results

The themes and views of family caregivers resonate with those of health care professionals. Their overlapping anxieties related to business-driven care homes, uncertainty of families when making EOL decisions and the importance of symptom management referring to contexts, mechanisms and outcomes, respectively. Contexts specific to family carers were ad hoc information about services, dementia progression and access to funding. Not all family carers identified dementia as terminal, but many recognised the importance of continuity of care and knowing the wishes of the person with dementia. New mechanisms included specific resources for improving EOL care and barriers to discussing and planning for future care. Family carers identified the importance of comfort, being present, the meeting of basic care needs and feeling the right decisions have been made as good outcomes of care.

Conclusions

Family carers and health care professionals share similar concerns about the challenges to good EOL dementia care. Better understanding of the effects of dementia at the advanced stages would improve confidence in EOL care and reduce uncertainty in decision making for family carers and health care professionals.
Efficacy of acupuncture in the management of post-apoplectic aphasia: a systematic review and meta-analysis of randomized controlled trials
Authors: Tang He-yong , Tang Wei , Yang Feng , Wu Wei-wei , Shen Guo-ming
Published: October 2019

Background

Aim of this study was to evaluate the effectiveness of scalp, tongue, and Jin’s 3-needle acupuncture for the improvement of postapoplectic aphasia.

Method

PubMed, Cochrane, Embase databases were searched using index words to identify qualifying randomized controlled trials (RCTs). Meta-analyses of odds ratios (OR) or standardized mean differences (SMD) were performed to evaluate the outcomes between investigational (scalp / tongue / Jin’s 3-needle acupuncture) and control (traditional acupuncture; TA and/or rehabilitation training; RT) groups.

Results

Thirty-two RCTs (1310 participants in investigational group and 1270 in control group) were included. Compared to TA, (OR 3.05 [95% CI: 1.77, 5.28];p<0.00001), tongue acupuncture (OR 3.49 [1.99, 6.11];p<0.00001), and Jin’s 3-needle therapy (OR 2.47 [1.10, 5.53];p = 0.03) had significantly better total effective rate. Compared to RT, scalp acupuncture (OR 4.24 [95% CI: 1.68, 10.74];p = 0.002) and scalp acupuncture with tongue acupuncture (OR 7.36 [3.33, 16.23];p<0.00001) had significantly better total effective rate. In comparison with TA/RT, scalp acupuncture, tongue acupuncture, scalp acupuncture with tongue acupuncture, and Jin’s three-needling significantly improved ABC, oral expression, comprehension, writing and reading scores.

Conclusion

As treatments to postapoplectic aphasia, scalp / tongue acupuncture and Jin’s Three-needling are found better than TA and/or RT in yielding total effective rate and improving ABC, oral expression, comprehension, reading and writing scores.