bluuebunny/crossref_metadata_2025 huggingface dataset:
The association of neutrophil-lymphocyte ratio and lymphocyte-monocyte ratio with 3-month clinical outcome after mechanical thrombectomy following stroke
Authors: Lux Danielle , Alakbarzade Vafa , Bridge Luke , Clark Camilla N. , Clarke Brian , Zhang Liqun , Khan Usman , Pereira Anthony C.
Published: February 2020

Background and aim

Neutrophil-lymphocyte ratio (NLR) and lymphocyte-monocyte ratio (LMR) are associated with clinical outcomes in malignancy, cardiovascular disease and stroke. Here we investigate their association with outcome after acute ischaemic stroke treated by mechanical thrombectomy (MT).

Methods

Patients were selected using audit data for MT for acute anterior circulation ischaemic stroke at a UK centre from May 2016–July 2017. Clinical and laboratory data including neutrophil, lymphocyte and monocyte count tested before and 24 h after MT were collected. Poor functional outcome was defined as modified Rankin Scale (mRS) of 3–6 at 3 months. Multivariable logistic regression analyses were performed to explore the relationship of NLR and LMR with functional outcome.

Results

One hundred twenty-one patients (mean age 66.4 ± 16.7, 52% female) were included. Higher NLR (adjusted OR 0.022, 95% CI, 0.009–0.34, p = 0.001) and lower LMR (adjusted OR − 0.093, 95% CI (− 0.175)−(− 0.012), p = 0.025) at 24-h post-MT were significantly associated with poorer functional outcome when controlling for age, baseline NIHSS score, infarct size, presence of good collateral supply, recanalisation and symptomatic intracranial haemorrhage on multivariate logistic regression. Admission NLR or LMR were not significant predictors of mRS at 3 months. The optimal cut-off values of NLR and LMR at 24-h post-MT that best discriminated poor outcome were 5.5 (80% sensitivity and 60% specificity) and 2.0 (80% sensitivity and 50% specificity), respectively on receiver operating characteristic curve analysis.

Conclusion

NLR and LMR tested at 24 h after ictus or intervention may predict 3-month functional outcome.
Habitat suitability analysis reveals high ecological flexibility in a “strict” forest primate
Authors: Hansen Malene Friis , Nawangsari Ventie Angelia , van Beest Floris M. , Schmidt Niels Martin , Stelvig Mikkel , Dabelsteen Torben , Nijman Vincent
Published: February 2020

Background

Research of many mammal species tends to focus on single habitats, reducing knowledge of ecological flexibility. The Javan lutung (Trachypithecus auratus) is considered a strict forest primate, and little is known about populations living in savannah. In 2017–2018, we investigated the density and distribution of Javan lutung in Baluran National Park, Indonesia. We conducted ad libitum follows and line transect distance sampling with habitat suitability analysis of Javan lutung.

Results

Estimated density was 14.91 individuals km− 2(95% CI 7.91–28.08), and estimated population size was 3727 individuals (95% CI 1979 – 7019). Long-tailed macaque (Macaca fascicularis) habitat suitability was the main driver of lutung habitat suitability as the probability of lutung occurrence increased greatly with macaque habitat suitability. Distance to roads, and distance to secondary forest had a negative relationship with lutung occurrence. Lutung habitat suitability decreased with increasing elevation, however, Mt Baluran and the primary forest on Mt Baluran was under-sampled due to treacherous conditions. Follows of six focus groups revealed considerable use of savannah, with terrestrial travel. The follows also revealed polyspecific associations with long-tailed macaques through shared sleeping sites and inter-specific vocalisations.

Conclusions

Our study provides new knowledge on the general ecology of Javan lutung, such as use of savannah habitats, underlining our need to branch out in our study sites to understand the flexibility and adaptability of our study species. Another undocumented behaviour is the polyspecific association with long-tailed macaques. We encourage more research on this subject.
Predictive model of the first failure pattern in patients receiving definitive chemoradiotherapy for inoperable locally advanced non-small cell lung cancer (LA-NSCLC)
Authors: Zhu Xueru , Hou Runping , Li Xiaoyang , Jiang Chang , Xia Wuyan , Fu Xiaolong
Published: February 2020

Purpose

To analyze patterns of failure in patients with LA-NSCLC who received definitive chemoradiotherapy (CRT) and to build a nomogram for predicting the failure patterns in this population of patients.

Materials and methods

Clinicopathological data of patients with LA-NSCLC who received definitive chemoradiotherapy and follow-up between 2013 and 2016 in our hospital were collected. The endpoint was the first failure after definitive chemoradiotherapy. With using elastic net regression and 5-fold nested cross-validation, the optimal model with better generalization ability was selected. Based on the selected model and corresponding features, a nomogram prediction model was built. This model was also validated by ROC curves, calibration curve and decision curve analysis (DCA).

Results

With a median follow-up of 28 months, 100 patients experienced failure. There were 46 and 54 patients who experience local failure and distant failure, respectively. Predictive model including 9 factors (smoking, pathology, location, EGFR mutation, age, tumor diameter, clinical N stage, consolidation chemotherapy and radiation dose) was finally built with the best performance. The average area under the ROC curve (AUC) with 5-fold nested cross-validation was 0.719, which was better than any factors alone. The calibration curve revealed a satisfactory consistency between the predicted distant failure rates and the actual observations. DCA showed most of the threshold probabilities in this model were with good net benefits.

Conclusion

Clinicopathological factors could collaboratively predict failure patterns in patients with LA-NSCLC who are receiving definitive chemoradiotherapy. A nomogram was built and validated based on these factors, showing a potential predictive value in clinical practice.
Comparison of the therapeutic outcomes between open plantar fascia release and percutaneous radiofrequency ablation in the treatment of intractable plantar fasciitis
Authors: Yuan Yusong , Qian Yuan , Lu Hao , Kou Yuhui , Xu Yangbo , Xu Hailin
Published: February 2020

Background

Heel pain is one of the most common complaints in foot and ankle clinic, and one of the leading causes of heel pain is plantar fasciitis.

Methods

A retrospective analysis was carried out in 31 cases (39 feet) of patients with intractable plantar fasciitis. In the enrolled 26 cases, 16 patients (19 feet) received open plantar fascia release, and the other 15 patients (20 feet) received percutaneous radiofrequency ablation. The surgical results were assessed by visual analog scale (VAS) and American Orthopaedic Foot and Ankle Society Ankle-Hindfoot Scale (AOFAS-AH) before and after surgery in all patients.

Results

All 31 patients were followed up successfully, with a mean follow-up time of 58.77 months. There were no differences of patient’s demographics and characteristics information between the two groups. The average operative time of the feet in the open plantar fascia release is longer than that in the percutaneous radiofrequency ablation. Furthermore, the percutaneous radiofrequency ablation group had a shorter recovery time to normal activity than the open plantar fascia release group. There were no differences of postoperative VAS scores and the AOFAS-AH scores between the two groups. All patients reported satisfaction after either operation.

Conclusion

The symptoms of pain and limb function were significantly improved in patients both of the partial plantar fascia release treated group and the percutaneous radiofrequency ablation treated group. The two types of surgical procedures shared the same long-term curative effects. However, percutaneous radiofrequency ablation was a better technique from the point of shorter operative time and postoperative recovery time.

Trial registration

Retrospectively registered.
Chromatographic fingerprints analysis and determination of seven components in Danmu preparations by HPLC–DAD/QTOF-MS
Authors: Li Nanxin , Zhang Jinju , Zhang Ying , Ma Zhiguo , Liao Jinhong , Cao Hui , Wu Menghua
Published: February 2020

Background

Danmu preparations (Danmu Capsule and Danmu Syrup), which are made from Nauclea officinalis stem extracts, have good clinical efficacy in acute tonsillitis, acute pharyngitis and upper respiratory tract infection. However, there is currently no reliable and systematic method to control the quality of these two Danmu preparations.

Methods

Using high-performance liquid chromatography (HPLC) coupled with diode array detection (DAD), the fingerprints of the Danmu preparations were established at 250 nm to comprehensively investigate the stability of preparation process. The chemical constituents in the Danmu preparations were separated and identified by HPLC coupled with quadrupole-time-of-flight high-definition mass spectrometry (HPLC–Q-TOF-MS). And seven major components were simultaneously determined at dual wavelengths (250 nm, 326 nm).

Results

The results of HPLC fingerprint similarity evaluation showed that the similarity values of 25 batches of Danmu preparations were more than 0.993. Twenty-three compounds, including 10 alkaloids, 6 phenolic acids, 2 iridoids, and 5 unknown compounds, were identified or tentatively characterized according to the retention times and MS/MS fragment patterns of compounds. The developed assay method of seven components was validated with acceptable linearity, precision, repeatability, stability and recovery. The contents of strictosamide belonging to alkaloids as the most abundant constituent in Danmu Capsule and Danmu Syrup were 43,681.20–99,652.49 μg/g and 1567.83–2427.25 μg/mL respectively. The contents of protocatechuic acid which were the highest in measured phenolic acids were 2633.01–7739.78 μg/g in Danmu Capsule and 192.05–448.71 μg/mL in Danmu Syrup, respectively. As an iridoid, the contents of sweroside in Danmu Capsule and Danmu Syrup were 1573.82–2789.81 μg/g and 70.32–182.81 μg/mL, respectively.

Conclusion

The established qualitative analysis method of fingerprint can be used to attain standardization, uniformity and stability of the preparation process. Meanwhile, the quantitative analysis in this study can be used as an accurate assay method for preparations.
The use of sodium DL-3-Hydroxybutyrate in severe acute neuro-metabolic compromise in patients with inherited ketone body synthetic disorders
Authors: Bhattacharya Kaustuv , Matar Walid , Tolun Adviye Ayper , Devanapalli Beena , Thompson Sue , Dalkeith Troy , Lichkus Kate , Tchan Michel
Published: February 2020

Background

Ketone bodies form a vital energy source for end organs in a variety of physiological circumstances. At different times, the heart, brain and skeletal muscle in particular can use ketones as a primary substrate. Failure to generate ketones in such circumstances leads to compromised energy delivery, critical end-organ dysfunction and potentially death. There are a range of inborn errors of metabolism (IEM) affecting ketone body production that can present in this way, including disorders of carnitine transport into the mitochondrion, mitochondrial fatty acid oxidation deficiencies (MFAOD) and ketone body synthesis. In situations of acute energy deficit, management of IEM typically entails circumventing the enzyme deficiency with replenishment of energy requirements. Due to profound multi-organ failure it is often difficult to provide optimal enteral therapy in such situations and rescue with sodium DL-3-hydroxybutyrate (S DL-3-OHB) has been attempted in these conditions as documented in this paper.

Results

We present 3 cases of metabolic decompensation, one with carnitine-acyl-carnitine translocase deficiency (CACTD) another with 3-hydroxyl, 3-methyl, glutaryl CoA lyase deficiency (HMGCLD) and a third with carnitine palmitoyl transferase II deficiency (CPT2D). All of these disorders are frequently associated with death in circumstance where catastrophic acute metabolic deterioration occurs. Intensive therapy with adjunctive S DL-3OHB led to rapid and sustained recovery in all. Alternative therapies are scarce in these situations.

Conclusion

S DL-3-OHB has been utilised in multiple acyl co A dehydrogenase deficiency (MADD) in cases with acute neurological and cardiac compromise with long-term data awaiting publication. The use of S DL-3-OHB is novel in non-MADD fat oxidation disorders and contribute to the argument for more widespread use.
Circulating cell-free mitochondrial DNA levels in Parkinson’s disease are influenced by treatment
Authors: Lowes Hannah , Pyle Angela , Santibanez-Koref Mauro , Hudson Gavin
Published: February 2020

Several studies have linked circulating cell-free mitochondrial DNA (ccf-mtDNA) to human disease. In particular, reduced ccf-mtDNA levels in the cerebrospinal fluid (CSF) of both Alzheimer’s and Parkinson’s disease (PD) patients have raised the hypothesis that ccf-mtDNA could be used as a biomarker for neurodegenerative disease onset and progression. However, how a reduction of CSF ccf-mtDNA levels relates to neurodegeneration remains unclear. Many factors are likely to influence ccf-mtDNA levels, such as concomitant therapeutic treatment and comorbidities. In this study we aimed to investigate these factors, quantifying CSF ccf-mtDNA from the Parkinson’s Progression Markers Initiative in 372 PD patients and 159 matched controls at two time points. We found that ccf-mtDNA levels appear significantly reduced in PD cases when compared to matched controls and are associated with cognitive impairment. However, our data indicate that this reduction in ccf-mtDNA is also associated with the commencement, type and duration of treatment. Additionally, we found that ccf-mtDNA levels are associated with comorbidities such as depression and insomnia, however this was only significant if measured in the absence of treatment. We conclude that in PD, similar to reports in HIV and sepsis, comorbidities and treatment can both influence ccf-mtDNA homeostasis, raising the possibility that ccf-mtDNA may be useful as a biomarker for treatment response or the development of secondary phenotypes. Given that, clinically, PD manifests often decades after neurodegeneration begins, predicting who will develop disease is important. Also, identifying patients who will respond to existing treatments or develop secondary phenotypes will have increased clinical importance as PD incidence rises.
Injury-related deaths before and during the Islamic State insurgency – Baghdad, Iraq, 2010–2015
Authors: Goers Matthew , Leidman Eva , Sultan Abdul-Salam Saleh , Hassan Ahmed , Bilukha Oleg
Published: February 2020

Background

Following a period of low intensity conflict during 2009–2012, the emergence of the Islamic State of Iraq and Levant (or Islamic State) in 2013 was associated with a resurgence of violence in Baghdad, Iraq’s capital and largest city. We evaluated trends in injury-related deaths in Baghdad before and during the Islamic State insurgency.

Methods

Iraqi National Injury Mortality Surveillance System prospectively collects information on fatal injuries from governorate coroner offices using standardized reporting forms. Trained coroner clerks collect information on victim demographics, intention of injury and mechanism of injury during medical examinations using reports from police and families. We analyzed data on all deaths reported by the Baghdad Forensic Institute from January 1, 2010 to December 31, 2015.

Results

There were 17,555 injury-related deaths with documented intent and mechanism (range 2385–3347 per year): 6241 from gunfire (36%), 1381 explosions (8%), 1348 non-gunfire assaults (8%), 3435 traffic accidents (20%), and 5150 other unintentional injuries (29%). Rates of gunfire (23.45 per 100,000) and explosion (5.90 per 100,000) deaths were significantly higher in 2014 than in all other years during the review period (p < 0.001 and p = 0.03, respectively). During the same period from 2010 to 2015, traffic accident deaths declined significantly from 13.29 to 6.35 (p = 0.002), with declines observed primarily among pedestrians. Trends in the rate of non-gunfire-assault and unintentional deaths, comparing 2010 and 2015, were not significant (p = 0.12 and p = 0.63, respectively). Unintentional deaths were mostly attributed to burns (46%) and electricity-related injuries (31%). The proportion of both females and children was highest in unintentional injury deaths.

Conclusions

During the study period, deaths from both gunfire and explosions in Baghdad peaked in 2014, corresponding with emergence of the Islamic State. Trends suggest a potential impact of insurgency-related activity on other injuries as evidenced by a decrease in the death rate from traffic accidents. The decreased traffic-related death rate could be from decreased vehicle and pedestrian activity during times of violence. Monitoring trends in injury mortality during conflict allows Iraq to identify priority injury causes to inform public health interventions.
Upregulation of Beta4 subunit of BKCa channels in the anterior cingulate cortex contributes to mechanical allodynia associated anxiety-like behaviors
Authors: Zhao Huan , Xue Qian , Li Cong , Wang Qingchuan , Han Shichao , Zhou Yongsheng , Yang Tao , Xie Yingli , Fu Hao , Lu Changbo , Meng Fancheng , Zhang Ming , Zhang Yan , Wu Xianglong , Wu Shengxi , Zhuo Min , Xu Hui
Published: February 2020

The anterior cingulate cortex (ACC) serves as a critical hub for the anxiety and pain perception. The large-conductance Ca2+-activated potassium channels, or BKCachannels, are ubiquitously expressed throughout the central nervous system including the cingulate cortex. However, what changes of cortical BKCachannels undergo in the ACC remains unknown in pain-related anxiety. In the present study, a significant upregulation of synaptic and non-synaptic BKCachannel accessory β4 subunits in the ACC was accompanied with pain-associated anxiety-like behaviors in the chronic compression of multiple dorsal root ganglia (mCCD) of the rat. NS1619, an opener of BKCachannels, significantly rescued the alteration of fAHP and AP duration of ACC pyramidal neurons in mCCD rats. The mRNA expression of BKCaβ4 subunits was extremely upregulated in the ACC after mCCD with the increased amount of both synaptic and non-synaptic BKCaβ4 subunit protein. Meanwhile, NS1619 reversed the enhanced AMPA receptor-mediated spontaneous excitatory postsynaptic current (sEPSC) frequency and the attenuated PPR of ACC neurons in mCCD rats. Local activation of BKCachannels in the ACC reversed mechanical allodynia and anxiety-like behaviors. These results suggest that the upregulation of postsynaptic and presynaptic BKCaβ4 subunit may contribute to neuronal hyperexcitability and the enhanced synaptic transmission in the ACC in neuropathic pain state, and then may result in anxiety-like behavior induced by neuropathic pain.
PoDFEd: Podiatrists and Diabetes Footcare Education Survey ‐ How do Australian podiatrists provide diabetes education?
Authors: Yuncken Julia , Haines Terrance , Stolwyk Renerus J. , Williams Cylie M.
Published: February 2020

Background

Podiatrists provide care and education to people with diabetes. This often includes the use of education relating to complications of the disease and how to prevent them. It is currently unknown how Australian podiatrists provide this education. This study aimed to describe the foot related diabetes education being delivered to people with diabetes within the Australian podiatry setting.

Methods

This cross‐sectional cohort study contacted Australian podiatrists to complete an online survey regarding their provision of diabetes education. The Qualtrics online survey application was advertised to Australian podiatrists via social media, at state conferences and through the Australian Podiatry Association and other similar association group emails. A multivariate stepwise progression was utilised to collate and decipher data. A chi‐squared test was used to determine significant links between podiatrist's method of education, demographic variables and topics of education.

Results

Findings linked the use of visual, written, generic handout and individualised handouts to various components of education and demographic information of Australian podiatrists. Verbal education had no significant links to demographic and topics of education relating to diabetes.

Conclusions

This paper discovered a range of topics covered and methods used by Australian podiatrists during consultations with patients with diabetes.
Protein velocity and acceleration from single-cell multiomics experiments
Authors: Gorin Gennady , Svensson Valentine , Pachter Lior
Published: February 2020

The simultaneous quantification of protein and RNA makes possible the inference of past, present, and future cell states from single experimental snapshots. To enable such temporal analysis from multimodal single-cell experiments, we introduce an extension of the RNA velocity method that leverages estimates of unprocessed transcript and protein abundances to extrapolate cell states. We apply the model to six datasets and demonstrate consistency among cell landscapes and phase portraits. The analysis software is available as the protaccel Python package.
Driving Pressure During General Anesthesia for Open Abdominal Surgery (DESIGNATION): study protocol of a randomized clinical trial
Authors:   The DESIGNATION–investigators
Published: February 2020

Background

Intraoperative driving pressure (ΔP) is associated with development of postoperative pulmonary complications (PPC). When tidal volume (VT) is kept constant, ΔP may change according to positive end-expiratory pressure (PEEP)-induced changes in lung aeration. ΔP may decrease if PEEP leads to a recruitment of collapsed lung tissue but will increase if PEEP mainly causes pulmonary overdistension. This study tests the hypothesis that individualized high PEEP, when compared to fixed low PEEP, protects against PPC in patients undergoing open abdominal surgery.

Methods

The “Driving prESsure durIng GeNeral AnesThesIa for Open abdomiNal surgery trial” (DESIGNATION) is an international, multicenter, two-group, double-blind randomized clinical superiority trial. A total of 1468 patients will be randomly assigned to one of the two intraoperative ventilation strategies. Investigators screen patients aged ≥ 18 years and with a body mass index ≤ 40 kg/m2, scheduled for open abdominal surgery and at risk for PPC. Patients either receive an intraoperative ventilation strategy with individualized high PEEP with recruitment maneuvers (RM) (“individualized high PEEP”) or one in which PEEP of 5 cm H2O without RM is used (“low PEEP”). In the “individualized high PEEP” group, PEEP is set at the level at which ΔP is lowest. In both groups of the trial, VTis kept at 8 mL/kg predicted body weight. The primary endpoint is the occurrence of PPC, recorded as a collapsed composite of adverse pulmonary events.

Discussion

DESIGNATION will be the first randomized clinical trial that is adequately powered to compare the effects of individualized high PEEP with RM versus fixed low PEEP without RM on the occurrence of PPC after open abdominal surgery. The results of DESIGNATION will support anesthesiologists in their decisions regarding PEEP settings during open abdominal surgery.

Trial registration

Clinicaltrials.gov,NCT03884543. Registered on 21 March 2019.
Correction to: The Invested in Diabetes Study Protocol: a cluster randomized pragmatic trial comparing standardized and patient-driven diabetes shared medical appointments
Authors: Kwan Bethany M. , Dickinson L. Miriam , Glasgow Russell E. , Sajatovic Martha , Gritz Mark , Holtrop Jodi Summers , Nease Don E. , Ritchie Natalie , Nederveld Andrea , Gurfinkel Dennis , Waxmonsky Jeanette A.
Published: February 2020

After publication of our article [1] the authors have notified us that the title for Figure 1 was incorrectly captioned.
Evaluating the re-identification risk of a clinical study report anonymized under EMA Policy 0070 and Health Canada Regulations
Authors: Branson Janice , Good Nathan , Chen Jung-Wei , Monge Will , Probst Christian , El Emam Khaled
Published: February 2020

Background

Regulatory agencies, such as the European Medicines Agency and Health Canada, are requiring the public sharing of clinical trial reports that are used to make drug approval decisions. Both agencies have provided guidance for the quantitative anonymization of these clinical reports before they are shared. There is limited empirical information on the effectiveness of this approach in protecting patient privacy for clinical trial data.

Methods

In this paper we empirically test the hypothesis that when these guidelines are implemented in practice, they provide adequate privacy protection to patients. An anonymized clinical study report for a trial on a non-steroidal anti-inflammatory drug that is sold as a prescription eye drop was subjected to re-identification. The target was 500 patients in the USA. Only suspected matches to real identities were reported.

Results

Six suspected matches with low confidence scores were identified. Each suspected match took 24.2 h of effort. Social media and death records provided the most useful information for getting the suspected matches.

Conclusions

These results suggest that the anonymization guidance from these agencies can provide adequate privacy protection for patients, and the modes of attack can inform further refinements of the methodologies they recommend in their guidance for manufacturers.
Rapid host expansion of an introduced parasite, the spiny rat louse Polyplax spinulosa (Psocodea: Phthiraptera: Polyplacidae), among endemic rodents in Australia
Authors: Wang Wei , Durden Lance A. , Shao Renfu
Published: February 2020

Background

Historical European exploration and colonization resulted in the introduction of four species of rodents to the Australian continent from Eurasia: the brown rat,Rattus norvegicus, the black rat,R. rattus, the Pacific rat,R. exulans, and the house mouse,Mus musculus. The spread of these rodents created opportunities for their co-introduced sucking lice to parasitize and adapt to endemic rodents in Australia.

Methods

We collected sucking lice from rodent specimens in seven museums across Australia. We identified the spiny rat louse,Polyplax spinulosa, based on morphology. We sequenced the mitochondrialcox1 andrrnLgenes ofP. spinulosaspecimens and constructed a phylogenetic tree withrrnLsequences.

Results

We examined 989 rodent specimens of 54 species and collected 2111 adult sucking lice and 1064 nymphal sucking lice. We found thatP. spinulosahad nearly doubled its host range by parasitizing at least six endemic rodent species in Australia. The other two introduced lice,P. serrataandHoplopleura pacifica, however, have apparently failed to expand to any endemic rodents in Australia. Our analysis of mitochondrialrrnLgene sequences dividedP. spinulosainto two genotypes (EuropeanvsSoutheast Asian), which differ by 7.5%; both genotypes were introduced into Australia and then expanded their host ranges to include endemic rodents.

Conclusions

The earliest record of a European ship landing in Australia was in 1606, followed by British settlement in 1788. The expansion ofP. spinulosato at least six endemic rodent species in Australia has therefore occurred in the time frame of 200 to 400 years, which is extremely rapid relative to its host expansion to eight native rat species in Eurasia in ~ 16 million years since it diverged fromP. serrata. The host expansion ofP. spinulosais remarkable for a blood-sucking louse and is in stark contrast to the absence of host expansion byP. serrataandH. pacifica. Comparison among these three introduced sucking lice indicated that both louse-specific factors and host-specific factors can contribute to the success or failure of host expansion.
Genetic differentiation and population structure of Anopheles funestus from Uganda and the southern African countries of Malawi, Mozambique, Zambia and Zimbabwe
Authors: Kaddumukasa Martha A. , Wright Jane , Muleba Mbanga , Stevenson Jenny C. , Norris Douglas E. , Coetzee Maureen
Published: February 2020

Background

Anopheles funestus(s.s.) is a primary vector of the malaria parasitePlasmodium falciparumin Africa, a human pathogen that causes almost half a million deaths each year. The population structure ofAn. funestuswas examined in samples from Uganda and the southern African countries of Malawi, Mozambique, Zambia and Zimbabwe.

Methods

Twelve microsatellites were used to estimate the genetic diversity and differentiation ofAn. funestusfrom 13 representative locations across five countries. These were comprised of four sites from Uganda, three from Malawi and two each from Mozambique, Zambia and Zimbabwe.

Results

All loci were highly polymorphic across the populations with high allelic richness and heterozygosity. A high genetic diversity was observed with 2–19 alleles per locus and an average number of seven alleles. Overall, expected heterozygosity (He) ranged from 0.65 to 0.79. When samples were pooled three of the 12 microsatellite loci showed Hardy–Weinberg equilibrium. Unsupervised Bayesian clustering analysis of microsatellite data revealed two clusters withAn. funestussamples from Mozambique, Uganda and Zambia falling into one group and Malawi and Zimbabwe into another. The overall genetic differentiation between the populations was moderate (FST = 0.116). Pairwise differentiation between the pairs was low but significant. A weak but significant correlation was established between genetic and geographical distance for most populations.

Conclusions

High genetic diversity revealed by the loci with low to moderate differentiation, identified two clusters among theAn. funestuspopulations. Further research on the population dynamics ofAn. funestusin east and southern Africa is essential to understand the implications of this structuring and what effect it may have on the efficient implementation of mosquito vector control strategies.
Functional characterization of acyl-CoA binding protein in Neospora caninum
Authors: Zhou Bingxin , Fu Yong , Zhang Heng , Wang Xianmei , Jin Gaowei , Xu Jianhai , Liu Qun , Liu Jing
Published: February 2020

Background

Lipid metabolism is pivotal for the growth of apicomplexan parasites. Lipid synthesis requires bulk carbon skeleton acyl-CoAs, the transport of which depends on the acyl-CoA binding protein (ACBP). In Neospora caninum, the causative agent of neosporosis, the FASII pathway is required for growth and pathogenicity. However, little is known about the fatty acid transport mechanism in N. caninum.

Methods

We have identified a cytosolic acyl-CoA binding protein, with highly conserved amino acid residues and a typical acyl-CoA binding domain in N. caninum. The recombinant NcACBP protein was expressed to verify the binding activities of NcACBP in vitro, and the heterologous expression of NcACBP in Δacbp yeast in vivo. Lipid extraction from ΔNcACBP or the wild-type of N. caninum was analyzed by GC-MS or TLC. Furthermore, transcriptome analysis was performed to compare the gene expression in different strains.

Results

The NcACBP recombinant protein was able to specifically bind acyl-CoA esters in vitro. A yeast complementation assay showed that heterologous expression of NcACBP rescued the phenotypic defects in Δacbp yeast, indicating of the binding activity of NcACBP in vivo. The disruption of NcACBP did not perturb the parasite’s growth but enhanced its pathogenicity in mice. The lipidomic analysis showed that disruption of NcACBP caused no obvious changes in the overall abundance and turnover of fatty acids while knockout resulted in the accumulation of triacylglycerol. Transcriptional analysis of ACBP-deficient parasites revealed differentially expressed genes involved in a wide range of biological processes such as lipid metabolism, posttranslational modification, and membrane biogenesis.

Conclusions

Our study demonstrated that genetic ablation of NcACBP did not impair the survival and growth phenotype of N. caninum but enhanced its pathogenicity in mice. This deletion did not affect the overall fatty acid composition but modified the abundance of TAG. The loss of NcACBP resulted in global changes in the expression of multiple genes. This study provides a foundation for elucidating the molecular mechanism of lipid metabolism in N. caninum.
Evaluation of RNA purification methods by using different blood stabilization tubes: identification of key features for epidemiological studies
Authors: Carrillo-Ávila J. A. , de la Puente R. , Catalina P. , Rejón J. D. , Espín-Vallejo L. , Valdivieso V. , Aguilar-Quesada R.
Published: February 2020

Objective

Peripheral blood is the most promising source of RNA biomarkers for diagnostic and epidemiological studies, because the presence of disease and prognostic information is reflected in the gene expression pattern. Quality RNA is used by a number of different downstream applications, so the selection of the most appropriate RNA stabilization and purification method is important. We have analyzed the RNA purified from 300 blood samples from 25 donors processed by two technicians using three methodologies with Tempus and PaxGene tubes.

Results

The best quality sample results were obtained with the Tempus Spin RNA Isolation Kit and the PaxGene Blood miRNA Kit, although larger amounts of RNA were obtained with the Tempus Spin RNA Isolation Kit. Lower Cq values were observed for RNA and miRNA genes in samples that were tested with PaxGene Blood miRNA Kit and Tempus Spin RNA Isolation Kit respectively. We identify the Tempus Spin RNA Isolation Kit as the most robust methodology, whilst the MagMax for Stabilized Blood Tubes RNA Isolation Kit showed the most instability. For biobanks, which process a large cohort and conduct epidemiological studies, the Tempus Spin RNA Isolation Kit is the most appropriate methodology. The study demonstrates the robustness of real-life procedures.
Prospective isolation of chondroprogenitors from human iPSCs based on cell surface markers identified using a CRISPR-Cas9-generated reporter
Authors: Dicks Amanda , Wu Chia-Lung , Steward Nancy , Adkar Shaunak S. , Gersbach Charles A. , Guilak Farshid
Published: February 2020

Background

Articular cartilage shows little or no capacity for intrinsic repair, generating a critical need of regenerative therapies for joint injuries and diseases such as osteoarthritis. Human-induced pluripotent stem cells (hiPSCs) offer a promising cell source for cartilage tissue engineering and in vitro human disease modeling; however, off-target differentiation remains a challenge during hiPSC chondrogenesis. Therefore, the objective of this study was to identify cell surface markers that define the true chondroprogenitor population and use these markers to purify iPSCs as a means of improving the homogeneity and efficiency of hiPSC chondrogenic differentiation.

Methods

We used a CRISPR-Cas9-editedCOL2A1-GFPknock-in reporter hiPSC line, coupled with a surface marker screen, to identify a novel chondroprogenitor population. Single-cell RNA sequencing was then used to analyze the distinct clusters within the population. An unpairedttest with Welch’s correction or an unpaired Kolmogorov-Smirnov test was performed with significance reported at a 95% confidence interval.

Results

Chondroprogenitors expressing CD146, CD166, and PDGFRβ, but not CD45, made up an average of 16.8% of the total population. Under chondrogenic culture conditions, these triple-positive chondroprogenitor cells demonstrated decreased heterogeneity as measured by single-cell RNA sequencing with fewer clusters (9 clusters in unsorted vs. 6 in sorted populations) closer together. Additionally, there was more robust and homogenous matrix production (unsorted: 1.5 ng/ng vs. sorted: 19.9 ng/ng sGAG/DNA;p < 0.001) with significantly higher chondrogenic gene expression (i.e.,SOX9,COL2A1,ACAN;p < 0.05).

Conclusions

Overall, this study has identified a unique hiPSC-derived subpopulation of chondroprogenitors that are CD146+/CD166+/PDGFRβ+/CD45−and exhibit high chondrogenic potential, providing a purified cell source for cartilage tissue engineering or disease modeling studies.
Insights into the roles of sperm in animal cloning
Authors: Qu Pengxiang , Wang Yongsheng , Zhang Chengsheng , Liu Enqi
Published: February 2020

Somatic cell nuclear transfer (SCNT) has shown a wide application in the generation of transgenic animals, protection of endangered animals, and therapeutic cloning. However, the efficiency of SCNT remains very low due to some poorly characterized key factors. Compared with fertilized embryos, somatic donor cells lack some important components of sperm, such as sperm small noncoding RNA (sncRNA) and proteins. Loss of these factors is considered an important reason for the abnormal development of SCNT embryo. This study focused on recent advances of SCNT and the roles of sperm in development. Sperm-derived factors play an important role in nucleus reprogramming and cytoskeleton remodeling during SCNT embryo development. Hence, considering the role of sperm may provide a new strategy for improving cloning efficiency.
Role and therapeutic effects of skeletal muscle-derived non-myogenic cells in a rat myocardial infarction model
Authors: Iseoka Hiroko , Miyagawa Shigeru , Saito Atsuhiro , Harada Akima , Sawa Yoshiki
Published: February 2020

Background

Transplantation of skeletal myoblast sheets is a promising strategy for the treatment of heart failure, and its therapeutic effects have already been proven in both animal disease models and clinical trials. Myoblast sheets reportedly demonstrate their therapeutic effects by producing many paracrine factors. Although the quality of processed cells for transplantation can be evaluated by the positive ratio of CD56, a myoblast marker, it is unclear which cell populations from isolated cells produce paracrine factors that have an impact on therapeutic effects, and whether these therapeutic effects are closely correlated with CD56-positive cells isolated from the skeletal muscle is also unclear. Therefore, we hypothesized that CD56-negative cells as well as CD56-positive cells isolated from the skeletal muscle produce paracrine factors and have therapeutic effects in skeletal muscle-derived cell sheet therapy for heart failure.

Methods

Cell surface and intracellular markers of CD56-negative non-myogenic cells (NMCs) and CD56-positive myoblasts were evaluated. We also analyzed cytokine expression, tube formation ability, and stem cell mobilization in both cell populations. Finally, we assessed the therapeutic effects of the cell populations in a rat myocardial infarction model.

Results

Analysis of cell surface and intracellular markers revealed that CD56-negative NMCs expressed fibroblast markers and a higher level of mesenchymal cell markers, such as CD49b and CD140a, than myoblasts. Both NMCs and myoblasts expressed various cytokines in vitro with different expression patterns. In addition, NMCs induced tube formation (control vs. myoblasts vs. NMCs: 100 ± 11.2 vs. 142 ± 8.3 vs. 198 ± 7.4%) and stem cell mobilization (control vs. myoblasts vs. NMCs: 100 ± 6.8 vs. 210 ± 22.9 vs. 351 ± 36.0%) to a higher degree in vitro than did myoblasts. The effect of NMCs and myoblasts on the improvement of cardiac function and suppression of myocardial fibrosis in rat myocardial infarction model was comparable.

Conclusion

These results indicate that NMCs exhibit therapeutic effects in skeletal muscle-derived cell sheet therapy for heart failure. Thus, accurate parameters correlating with therapeutic effects need to be further explored.
A cytokine screen using CRISPR-Cas9 knock-in reporter pig iPS cells reveals that Activin A regulates NANOG
Authors: Xu Junjun , Zheng Zheng , Du Xuguang , Shi Bingbo , Wang Jichang , Gao Dengfeng , Zhu Qianqian , Chen Xinze , Han Jianyong
Published: February 2020

Background

NANOGfunctions as the gateway for the generation of pluripotent stem cells (PSCs) in mice and humans. NANOG is a transcription factor highly expressed in pig pre-implantation embryos, indicating that it is a conserved pluripotency-associated factor. However, pigNANOGreporter PSCs have yet to be established, and the regulation of pluripotency byNANOGis not fully understood in this animal.

Methods

In this study, pigNANOGtdTomato knock-in reporter positive PC-iPS cells were established using CRISPR/Cas9. The resulting cell line was treated with several cytokines and their corresponding inhibitors to identify pathways that regulateNANOGexpression. The pathways examined were LIF (leukemia inhibitory factor)/IL6 (interleukin 6)-STAT3, FGF (fibroblast growth factor)/ERK, IGF1 (insulin-like growth factor 1)/PIP3 (phosphoinositide 3-kinase)-AKT, Activin A/SMAD, and BMP4 (bone morphogenetic proteins)/SMAD.

Results

Our experiments showed that the Activin A/SMAD pathway is directly associated with activation ofNANOGexpression in the pig, as is also the case in mice and humans. Activin A directly regulates the expression of pigNANOGvia SMAD2/3; inhibition of this pathway by SB431542 resulted in inhibition of NANOG expression.

Conclusions

Our results show that Activin A plays an important regulatory role in NANOG-mediated pluripotency in pig iPS cells. Activin A treatment may be therefore an effective method for de novo derivation of authentic embryonic stem cells (ESCs) from pig pre-implantation embryos.
Uncertainty quantification with risk measures in production planning
Authors: Göttlich Simone , Knapp Stephan
Published: February 2020

This paper is concerned with a simulation study for a stochastic production network model, where the capacities of machines may change randomly. We introduce performance measures motivated by risk measures from finance leading to a simulation based optimization framework for the production planning. The same measures are used to investigate the scenario when capacities are related to workers that are randomly not available. This corresponds to the study of a workforce planning problem in an uncertain environment.
Correction to: Practising an explosive eruption in Iceland: outcomes from a European exercise
Authors: Witham Claire , Barsotti Sara , Dumont Stéphanie , Oddsson Björn , Sigmundsson Freysteinn
Published: February 2020

Following publication of the original article Witham et al., 2020, it was noticed a mistake of copyright holder name.
Neimark–Sacker bifurcation and the generate cases of Kopel oligopoly model with different adjustment speed
Authors: Li Bo , He Qizhi , Chen Ruoyu
Published: February 2020

In this paper, bifurcations and chaotic behaviours of Kopel oligopoly model with different adjustment speed are discussed. The results imply that the Kopel oligopoly model undergoes flip bifurcation, Neimark–Sacker bifurcation, 1:3 and 1:4 resonances, which could induce complex dynamics, especially global behaviours between different orbits. The conditions for the occurrence of three different kinds of bifurcation are derived. Furthermore, the numerical simulations provide us the case study of theoretical analysis and the corresponding dynamical behaviours, especially the occurrence of global orbits.
Note on the persistence and stability property of a stage-structured prey–predator model with cannibalism and constant attacking rate
Authors: Chen Fengde , Deng Hang , Zhu Zhenliang , Li Zhong
Published: February 2020

We revisit the persistence and stability property of a stage-structured prey–predator model with cannibalism and constant attacking rate. By using the differential inequality theory and Bendixson–Dulac criterion, we show that if the system without cannibalism is permanent, then the system with cannibalism is also permanent. By developing some new analysis technique, we obtain a new set of sufficient conditions which ensure the global asymptotic stability of the nonnegative equilibrium, which means that, under some suitable assumption, prey cannibalism has no influence on the stability property of the predator free equilibrium. Our results essentially improve the corresponding results of Limin Zhang and Chaofeng Zhang.
Effectiveness of a structured, framework-based approach to implementation: the Researching Effective Approaches to Cleaning in Hospitals (REACH) Trial
Authors: Hall Lisa , White Nicole M. , Allen Michelle , Farrington Alison , Mitchell Brett G. , Page Katie , Halton Kate , Riley Thomas V. , Gericke Christian A. , Graves Nicholas , Gardner Anne
Published: February 2020

Background

Implementing sustainable practice change in hospital cleaning has proven to be an ongoing challenge in reducing healthcare associated infections. The purpose of this study was to develop a reliable framework-based approach to implement and quantitatively evaluate the implementation of evidence-based practice change in hospital cleaning.

Design/methods

The Researching Effective Approaches to Cleaning in Hospitals (REACH) trial was a pragmatic, stepped-wedge randomised trial of an environmental cleaning bundle implemented in 11 Australian hospitals from 2016 to 2017. Using a structured multi-step approach, we adapted the integrated Promoting Action on Research Implementation in Health Services (i-PARIHS) framework to support rigorous and tailored implementation of the cleaning bundle intervention in eleven diverse and complex settings. To evaluate the effectiveness of this strategy we examined post-intervention cleaning bundle alignment calculated as a score (an implementation measure) and cleaning performance audit data collected using ultraviolet (UV) gel markers (an outcome measure).

Results

We successfully implemented the bundle and observed improvements in cleaning practice and performance, regardless of hospital size, intervention duration and contextual issues such as staff and organisational readiness at baseline. There was a positive association between bundle alignment scores and cleaning performance at baseline. This diminished over the duration of the intervention, as hospitals with lower baseline scores were able to implement practice change successfully.

Conclusion

Using a structured framework-based approach allows for pragmatic and successful implementation of clinical trials across diverse settings, and assists with quantitative evaluation of practice change.

Trial registration

Australia New Zealand Clinical Trial Registry ACTRN12615000325505, registered on 4 September 2015.
What bereaved parents want health care providers to know when their babies are stillborn: a community-based participatory study
Authors: Farrales Lynn L. , Cacciatore Joanne , Jonas-Simpson Christine , Dharamsi Shafik , Ascher Jaime , Klein Michael C.
Published: February 2020

Background

Bereaved parents experience higher rates of depressive and post-traumatic stress symptoms after the stillbirth of a baby than after live-birth. Yet, these effects remain underreported in the literature and, consequently, insufficiently addressed in health provider education and practice. We conducted a participatory based study to explore the experiences of grieving parents during their interaction with health care providers during and after the stillbirth of a baby.

Methods

This community-based participatory study utilized four focus groups comprised of twenty-seven bereaved parents (44% fathers). Bereaved parents conceptualized the study, participating at all stages of research, analyses, and drafting. Data were reduced into a main theme and subthemes, then broad-based member checked to ensure fidelity and nuances within themes.

Results

The major theme that emerged centered on provider acknowledgement of the baby as an irreplaceable individual. Subthemes reflected 1) acknowledgement of parenthood and grief, 2) recognition of the traumatic nature of stillbirth, and 3) acknowledgement of enduring grief coupled with access to support. It was important that providers realized how grief was experienced within health care and social support systems, concretized by their desire for long-term, specialized support.

Conclusions

Both mothers and fathers feel that acknowledgement of their baby as an individual, their parenthood, and their enduring traumatic grief by healthcare providers are key elements required in the process of initiating immediate and ongoing care after the stillbirth of a baby.