bluuebunny/crossref_metadata_2025 huggingface dataset:
SPAligner: alignment of long diverged molecular sequences to assembly graphs
Authors: Dvorkina Tatiana , Antipov Dmitry , Korobeynikov Anton , Nurk Sergey
Published: July 2020

Background

Graph-based representation of genome assemblies has been recently used in different contexts — from improved reconstruction of plasmid sequences and refined analysis of metagenomic data to read error correction and reference-free haplotype reconstruction. While many of these applications heavily utilize the alignment of long nucleotide sequences to assembly graphs, first general-purpose software tools for finding such alignments have been released only recently and their deficiencies and limitations are yet to be discovered. Moreover, existing tools can not perform alignment of amino acid sequences, which could prove useful in various contexts — in particular the analysis of metagenomic sequencing data.

Results

In this work we present a novel SPAligner (Saint-Petersburg Aligner) tool for aligning long diverged nucleotide and amino acid sequences to assembly graphs. We demonstrate that SPAligner is an efficient solution for mapping third generation sequencing reads onto assembly graphs of various complexity and also show how it can facilitate the identification of known genes in complex metagenomic datasets.

Conclusions

Our work will facilitate accelerating the development of graph-based approaches in solving sequence to genome assembly alignment problem. SPAligner is implemented as a part of SPAdes tools library and is available on Github.
Amino acid sequence associated with bacteriophage recombination site helps to reveal genes potentially acquired through horizontal gene transfer
Authors: Daugavet Maria A. , Shabelnikov Sergey V. , Podgornaya Olga I.
Published: July 2020

Background

Horizontal gene transfer, i.e. the acquisition of genetic material from nonparent organism, is considered an important force driving species evolution. Many cases of horizontal gene transfer from prokaryotes to eukaryotes have been registered, but no transfer mechanism has been deciphered so far, although viruses were proposed as possible vectors in several studies. In agreement with this idea, in our previous study we discovered that in two eukaryotic proteins bacteriophage recombination site (AttP) was adjacent to the regions originating via horizontal gene transfer. In one of those cases AttP site was present inside the introns of cysteine-rich repeats. In the present study we aimed to apply computational tools for finding multiple horizontal gene transfer events in large genome databases. For that purpose we used a sequence of cysteine-rich repeats to identify genes potentially acquired through horizontal transfer.

Results

HMMER remote similarity search significantly detected 382 proteins containing cysteine-rich repeats. All of them, except 8 sequences, belong to eukaryotes. In 124 proteins the presence of conserved structural domains was predicted. In spite of the fact that cysteine-rich repeats are found almost exclusively in eukaryotic proteins, many predicted domains are most common for prokaryotes or bacteriophages. Ninety-eight proteins out of 124 contain typical prokaryotic domains. In those cases proteins were considered as potentially originating via horizontal transfer. In addition, HHblits search revealed that two domains of the same fungal protein, Glycoside hydrolase and Peptidase M15, have high similarity with proteins of two different prokaryotic species, hinting at independent horizontal gene transfer events.

Conclusions

Cysteine-rich repeats in eukaryotic proteins are usually accompanied by conserved domains typical for prokaryotes or bacteriophages. These proteins, containing both cysteine-rich repeats, and characteristic prokaryotic domains, might represent multiple independent horizontal gene transfer events from prokaryotes to eukaryotes. We believe that the presence of bacteriophage recombination site inside cysteine-rich repeat coding sequence may facilitate horizontal genes transfer. Thus computational approach, described in the present study, can help finding multiple sequences originated from horizontal transfer in eukaryotic genomes.
An unusual Staphylococcus saccharolyticus spondylodiscitis post kyphoplasty: a case report
Authors: Trojani Marie-Charlotte , Lamy Brigitte , Ruimy Raymond , Amoretti Nicolas , Risso Karine , Roux Christian
Published: July 2020

Background

Staphylococcus saccharolyticus is a rarely encountered coagulase-negative, which grows slowly and its strictly anaerobic staphylococcus from the skin. It is usually considered a contaminant, but some rare reports have described deep-seated infections. Virulence factors remain poorly known, although, genomic analysis highlights pathogenic potential.

Case presentation

We report a case of Staphylococcus saccharolyticus spondylodiscitis that followed kyphoplasty, a procedure associated with a low rate but possible severe infectious complication (0.46%), and have reviewed the literature. This case specifically stresses the risk of healthcare-associated S. saccharolyticus infection in high-risk patients (those with a history of alcoholism and heavy smoking).

Conclusion

S. saccharolyticus infection is difficult to diagnose due to microbiological characteristics of this bacterium; it requires timely treatment, and improved infection control procedure should be encouraged for high-risk patients.
Outcomes of arteriovenous access among cancer patients requiring chronic haemodialysis
Authors: Jeong Seonjeong , Kwon Hyunwook , Chang Jai Won , Han Youngjin , Kwon Tae-Won , Cho Yong-Pil
Published: July 2020

Background

There are limited data focusing specifically on the types of arteriovenous (AV) access used and outcomes of AV access among cancer patients as a consequence of cancer. We aimed to describe outcomes of AV access among cancer patients requiring chronic haemodialysis, and also to compare outcomes between patients with and without cancer.

Methods

In this single-centre, retrospective, observational cohort study, 84 patients diagnosed with cancer before AV access placement were included; we analysed outcomes of AV access among these patients and compared these outcomes with our previous results. The study endpoints were AV access patency and early failure, defined as AV access abandonment within 12 months after AV access placement.

Results

Various cancer types, stages, and treatments were identified in our analysis. Autologous arteriovenous fistulas (AVFs) were used for 92.9% of this study population. Using our previous results for comparison, we found no significant difference in death-censored primary (P = 0.546) and secondary (P = 0.266) patency of AV access between patients with and without cancer; however, the rate of early AVF failure was statistically significantly higher among cancer patients (25.6% vs 13.9%; P = 0.008), and the most common cause of AVF failure was patient death. The rate of early failure was significantly higher among patients with advanced-stage cancer (59.1%) than among those with early-stage cancer (12.9%) (P <  0.001).

Conclusions

Although AV access patency rates were similar among patients with and without cancer in the death-censored analysis, cancer patients were more prone to early AVF failure, mainly due to cancer-associated deaths, and this consideration needs to be carefully balanced against individual patients’ life expectancies, according to cancer type and stage.
Functional evaluation with microperimetry in large idiopathic macular holes treated by a free internal limiting membrane flap tamponade technique
Authors: Huang Peirong , Wang Hong , Chen Fenge , Chen Jieqiong , Hu Yifan , Sun Junran , Feng Jingyang , Zhu Hong
Published: July 2020

Background

Free internal limiting membrane (ILM) flap tamponade technique is an alternative choice for treating large idiopathic macular holes (IMHs). However, the functional recovery related to this surgical approach is not well-characterized. This study aimed to evaluate morphological and microperimetric outcomes 6 months after free ILM flap tamponade technique for large IMHs.

Methods

Twenty-two patients (22 eyes) with large IMHs (minimal diameter > 400 μm) were retrospectively enrolled in this study. All patients underwent 23-gauge pars plana vitrectomy with ILM peeling and free ILM flap tamponade procedures. Snellen best-corrected visual acuity (BCVA), optical coherence tomography (OCT), and MP-1 microperimetry were measured at baseline and 6 months after surgery. Associations of postoperative BCVA with retinal sensitivity were detected.

Results

Macular hole closure was achieved in 21 eyes (95.5%). Dislodgement of free ILM flap was found in non-closed eye. Mean logMAR BCVA improved from 1.10 ± 0.33 at baseline to 0.67 ± 0.32 at 6 months postoperatively (P < 0.001). The mean overall macular sensitivity and foveal fixation stability increased respectively from 8.58 ± 3.05 dB and 65.64 ± 17.28% before surgery to 11.55 ± 2.72 dB and 78.59 ± 13.00% at 6 months after surgery (P < 0.001). The mean change in foveal sensitivity (within 2°) was significantly greater than the change achieved for peri-foveal sensitivity (2° to 10°) by 1.50 ± 2.62 dB (P = 0.014). Linear regression analysis showed that postoperative logMAR BCVA was significantly associated with duration of symptom (B = 0.063, P = 0.001), preoperative logMAR BCVA (B = 0.770, P = 0.000), preoperative peri-foveal (B = − 0.065, P = 0.000) and foveal sensitivity (B = − 0.129, P = 0.000). Moreover, multiple regression model revealed that preoperative foveal sensitivity was independently associated with postoperative logMAR BCVA (B = − 0.430, P = 0.040).

Conclusions

Vitrectomy combined with ILM peeling and free ILM flap tamponade technique results in effective morphological and functional recovery for large IMHs. Preoperative foveal sensitivity might be a prognostic indicator for postoperative BCVA.
Timing of liver transplantation for pediatric acute liver failure due to mushroom poisoning: a case report and literature review
Authors: Yang Chun-Feng , Sheng Chu-Qiao , Ao Yu , Li Yu-Mei
Published: July 2020

Background

Pediatric acute liver failure is a rare, life-threatening illness. Mushroom poisoning is a rare etiology. For patients with irreversible pediatric acute liver failure, liver transplantation is the ultimate lifesaving therapy. However, it is difficult to determine the optimal timing of transplantation. Here, we present a case of pediatric acute liver failure due to mushroom poisoning in northeastern China. He was treated with liver transplantation and recovered. To our knowledge, there are few reports about liver transplantation for pediatric acute liver failure caused by mushroom poisoning in mainland China.

Case presentation

The patient was a previously healthy 9-year-old boy who gradually developed nausea, vomiting, jaundice and coma within 5 days after ingesting mushrooms. He was diagnosed with mushroom poisoning and acute liver failure. He was treated with conservative care but still deteriorated. On the 7th day after poisoning, he underwent LT due to grade IV hepatic encephalopathy. Twenty days later, he recovered and was discharged. A review of the literature revealed that the specific criteria and optimal timing of transplantation remain to be determined.

Conclusions

Patients with pediatric acute liver failure should be transferred to a center with a transplant unit early. Once conservative treatment fails, liver transplantation should be performed.
Patient-reported outcomes in major depressive disorder with suicidal ideation: a real-world data analysis using PatientsLikeMe platform
Authors: Borentain Stephane , Nash Abigail I. , Dayal Rachna , DiBernardo Allitia
Published: July 2020

Background

The current analysis utilized data collected via an online patient community platform, PatientsLikeMe (PLM) to compare patient-reported experiences in patients with major depressive disorder (MDD) with suicidal ideation (MDSI) to those with MDD but without suicidal ideation.

Methods

PLM members who joined PLM between May-2007 and February-2018 and reported a diagnosis of MDD were included. The MDSI cohort included patients with MDD who reported at least one suicide-related symptom at a severity greater than “none”. Demographics, comorbidities, symptoms, and side-effects were compared between MDSI and MDD cohorts. Factors correlated with suicidal ideation (SI) were determined by a random forest procedure.

Results

Patients in the MDSI cohort (n = 266) were younger (median age, 36 vs 44 years) with an earlier disease onset (before 30 years, 83% vs 71%), and a longer diagnosis latency (median, 4 vs 2 years) vs patients in the MDD cohort (n = 11,963). Majority of patients were women in both cohorts (73% vs 83%). Median number of psychiatric comorbidities was higher in the MDSI cohort (4 vs 3). Unprompted symptoms (e.g., loneliness, feeling of hopelessness, social anxiety, impulsivity, and self-hating thoughts) were more frequent in the MDSI cohort. Hopelessness, loneliness, anhedonia, social anxiety, and younger age were highly correlated with suicidal ideation.

Conclusions

This analysis utilized patient-reported data to better understand symptoms, experiences, and characteristics of patients with MDSI compared to patients with MDD. The results identified various risk factors correlated with suicidal ideation that may help guide clinical judgement for patients with MDD who may not voluntarily report suicidal ideation.
Randomized control trial of advanced cancer patients at a private hospital in Kenya and the impact of dignity therapy on quality of life
Authors: Weru John , Gatehi Miriam , Musibi Alice
Published: July 2020

Background

Palliative care is a modality of treatment that addresses physical, psychological and spiritual symptoms. Dignity therapy, a form of psychotherapy, was developed by Professor Harvey Chochinov, MD in 2005.The aim of the study was to assess the effect of one session of dignity therapy on quality of life in advanced cancer patients.

Methods

This was a randomized control trial of 144 patients (72 in each arm) randomized into group 1 (intervention arm) and group 2 (control arm). Baseline ESAS scores were determined in both arms following which group 1 received Dignity therapy while Group 2 received usual care only. Data collected was presented as printed (Legacy) documents to group 1 participants. These documents were a summary of previous discussions held. Post intervention ESAS scores were obtained in both groups after 6 weeks. Analysis was based on the intention to treat principle and descriptive statistics computed. The main outcome was symptom distress scores on the ESAS (summated out of 100 and symptom specific scores out of 10). The student T-test was used to test for difference in ESAS scores at follow up and graphs were computed for common cancers and comorbidities.

Results

Of the 144 (72 patients in each arm) patients randomized, 70%were female while 30% were male with a mean age of 50 years. At 6 weeks, 11 patients were lost to follow up, seven died and 126 completed the study. The commonly encountered cancers were gastrointestinal cancers (43%, p = 0.29), breast cancer (27.27% p = 0.71) and gynaecologic cancers (23% p = 0.35). Majority of the patients i.e. 64.3% had no comorbidities.

The primary analysis results showed higher scores for the DT group (change in mean = 1.57) compared to the UC group (change in mean = − 0.74) yielding a non-statistically significant difference in change scores of 1.44 (p = 0.670; 95% CI − 5.20 to 8.06). After adjusting for baseline scores, the mean (summated) symptom distress score was not significant (GLM p = 0.78). Dignity therapy group showed a trend towards statistical improvement in anxiety (p = 0.059). The largest effects seen were in improvement of appetite, lower anxiety and improved wellbeing (Cohen effect size 0.3, 0.5 and 0.31 respectively).

Conclusion

Dignity therapy showed no statistical improvement in overall quality of life. Symptom improvement was seen in anxiety and this was a trend towards statistical significance (p = 0.059).

Trial registration

Trial registration number PACTR201604001447244 retrospectively registered with Pan African Clinical trials on 28th January 2016.
RETRACTED ARTICLE: Curcumin inhibits the migration of osteoclast precursors and osteoclastogenesis by repressing CCL3 production
Authors: Liang Zhengeng , Xue Yan , Wang Tao , Xie Qi , Lin Jiafu , Wang Yu
Published: July 2020

Background

Curcumin can inhibit the osteoclastogenesis and the migration of several cells including macrophages. Osteoclast precursors (OCPs) are known to exist as bone marrow-derived macrophages (BMMs). This study aims to explore whether curcumin can prevent the fusion and differentiation of OCPs to mature osteoclasts by inhibiting OCP migration.

Methods

In this study, we investigated the role of curcumin in regulating the production of several chemokines (CCL2, CCL3 and CX3CL1) and the migration of OCPs by ELISA, Western blotting and Transwell assays. Furthermore, we explored the role of curcumin in the chemokines-related osteoclastogenesis using pharmacological intervention and virus infection, and used ovariectomized (OVX) mice (osteoporosis model) to explore the effect of curcumin on the production of specific chemokine in vivo.

Results

The results showed that curcumin significantly reduced the production of CCL3 in OCPs. Moreover, curcumin-inhibited the migration of OCPs was not affected by CCR1 (Receptor of CCL3) overexpression. Remarkably, curcumin-reduced osteoclastogenesis was significantly reversed by CCL3 addition, while CCR1 overexpression did not increase the osteoclastogenesis in the presence of curcumin. Furthermore, in vivo assays also showed that curcumin significantly reduced the production of CCL3 in OCPs in the trabecular bone of OVX mice.

Conclusions

In conclusion, curcumin prevents the migration of OCPs by reducing CCL3 production, ultimately inhibiting the formation of mature osteoclasts. Therefore, our study provides the clues for improving the clinical strategies of osteoporosis, dental implantation or orthodontic treatment.
Patient expectations, experiences and satisfaction with nintedanib and pirfenidone in idiopathic pulmonary fibrosis: a quantitative study
Authors: Moor C. C. , Mostard R. L. M. , Grutters J. C. , Bresser P. , Aerts J. G. J. V. , Dirksen C. D. , Kimman M. L. , Wijsenbeek M. S.
Published: July 2020

Background

Two antifibrotic drugs, nintedanib and pirfenidone, are available for treatment of idiopathic pulmonary fibrosis (IPF). Although efficacy and adverse events have been well studied, little is known about patient experiences with these drugs. We aimed to systematically and quantitatively evaluate patient expectations, experiences, and satisfaction with nintedanib and pirfenidone. Furthermore, we assessed which factors were associated with overall patient satisfaction with medication.

Methods

Outpatients with IPF prospectively completed the Patient Experiences and Satisfaction with Medication (PESaM) questionnaire before start, and after three and 6 months of antifibrotic treatment, as part of a randomized eHealth trial (NCT03420235). The PESaM questionnaire consists of an expectation module, a validated generic module evaluating patient experiences and satisfaction concerning the effectiveness, side-effects, and ease of use of a medication, and a disease-specific module about IPF. Satisfaction was scored on a scale from − 5 (very dissatisfied) to + 5 (very satisfied).

Results

In total, 90 patients were included, of whom 43% used nintedanib and 57% pirfenidone. After 6 months, the mean overall score for satisfaction with medication was 2.1 (SD 1.9). No differences were found in experiences and satisfaction with medication, and the number and severity of side-effects between nintedanib and pirfenidone. Perceived effectiveness of medication was rated as significantly more important than side-effects and ease of use (p = 0.001). Expectations of patients regarding effectiveness were higher than experiences after 6 months. Self-reported experience with effectiveness was the main factor associated with overall medication satisfaction.

Conclusions

Patient experiences and satisfaction with antifibrotic treatment were fairly positive, and similar for nintedanib and pirfenidone. Systematic evaluation of patient expectations, experiences, and satisfaction with medication could enhance shared-decision making and guide drug treatment decisions in the future.

Trial registration

NCT03420235.
Uptake, translocation and biotransformation of selenium nanoparticles in rice seedlings (Oryza sativa L.)
Authors: Wang Kang , Wang Yaqi , Li Kui , Wan Yanan , Wang Qi , Zhuang Zhong , Guo Yanbin , Li Huafen
Published: July 2020

Background

Selenium (Se) in soil mainly consists of selenite, selenate, and elemental Se. However, little is known about the mechanism involved in the uptake and biotransformation of elemental Se by plants.

Results

In this study, the uptake, translocation, subcellular distribution and biotransformation of selenium nanoparticles (SeNPs) in rice (Oryza sativa L.), and a comparison with selenite and selenate, were investigated through hydroponic experiments. The study revealed that SeNPs could be absorbed by rice plants; and aquaporin inhibitor was responsible for a 60.4% inhibition of SeNP influx, while metabolic inhibitor was ineffective. However, the SeNPs uptake rate of rice roots was approximately 1.7 times slower than that of selenite or selenate. Under the SeNPs or selenite treatment, Se was primarily accumulated in roots rather than in shoots, whereas an opposite trend was observed with selenate treatment. Additionally, most of the absorbed Se was distributed in cell wall of the SeNPs or selenite treated-rice plants, while its proportion was the highest in soluble cytosol of the selenate treated-rice plants. The absorbed SeNPs or selenite was rapidly assimilated to organic forms, with SeMet being the most predominant species in both shoots and roots of the rice plants. However, following selenate treatment, Se(VI) remained as the most predominant species, and only a small amount of it was converted to organic forms.

Conclusion

Therefore, this study provides a deeper understanding of the mechanisms associated SeNPs uptake and biotransformation within plants.
Extra-gastrointestinal stromal tumor arising in the lesser omentum with a platelet-derived growth factor receptor alpha (PDGFRA) mutation: a case report and literature review
Authors: Kanamori Kohei , Yamagata Yukinori , Honma Yoshitaka , Date Keiichi , Wada Takeyuki , Hayashi Tsutomu , Otsuki Sho , Sekine Shigeki , Yoshikawa Takaki , Katai Hitoshi , Nishida Toshiro
Published: July 2020

Background

Gastrointestinal stromal tumors (GIST) arising from sites other than the gastrointestinal (GI) tract, termed extra-gastrointestinal stromal tumors (EGIST), are rare. Among EGIST, those with platelet-derived growth factor receptor alpha (PDGFRA) mutations are even rarer, with only a few cases reported. About 80% of GIST has KIT mutations, and 10% of GIST have PDGFRA mutations, which commonly affect the TK2 domain (exon 18). Among the exon 18 mutations, the D842V substitution is limited to gastric GIST. In EGIST, the degree of KIT and PDGFRA mutations varies on where the location of the tumor is, and it is suggested that omental EGIST is similar to gastric GIST. Adjuvant imatinib therapy is recommended for high-risk GIST; however, it is known that imatinib is less effective against GIST with a PDGFRA D842V mutation.

Case presentation

A 75-year-old man was referred to our hospital with an extrinsic tumor of the lesser curvature of the gastric body. Intraoperative findings showed a tumor located outside of the lesser omentum with no connection between the tumor and the gastric wall. The tumor was subsequently resected. Pathological examination indicated a GIST arising in the lesser omentum measuring 70 mm in its longer dimension. Because the tumor had a PDGFRA mutation (D842V substitution), imatinib was suspected to lack efficacy to the tumor. Thus, although the tumor was considered clinically to have a high risk of recurrence, adjuvant imatinib therapy was not indicated. The patient has been free of recurrence for 29 months since the surgery.

Conclusion

We described a case of EGIST with a PDGFRA mutation arising in the lesser omentum. And we reviewed 57 cases of omental EGIST and showed that the clinicopathological characteristics and mutation status in omental EGIST were very similar to gastric GIST. In particular, PDGFAR D842V mutation rate in omental EGIST seemed as high as that in gastric GIST. These results suggested that omental EGIST is strongly related to gastric GIST, so the behavior of omental EGIST might be akin to gastric GIST. However, further studies are required to determine the prognosis and the necessity of adjuvant therapy for EGIST with a PDGFRA mutation.
AMPK activation overcomes anti-EGFR antibody resistance induced by KRAS mutation in colorectal cancer
Authors: Ye Hua , Liu Yi , Wu Kefeng , Luo Hui , Cui Liao
Published: July 2020

Background

Colorectal cancer (CRC) is associated with resistance to anti-epidermal growth factor receptor (EGFR) antibodies (both acquired and intrinsic), owing to the amplification or mutation of the KRAS oncogene. However, the mechanism underlying this resistance is incompletely understood.

Methods

DLD1 cells with WT (+/−) or KRAS G13D mutant allele were treated with different concentrations of Cetuximab (Cet) or panitumumab (Pab) to study the mechanism underlying the KRAS mutation-induced resistance to anti-EGFR antibodies. The function of AMPK in KRAS mutation-induced resistance to anti-EGFR antibodies in CRC cells, and the regulatory role of Bcl-2 family proteins in DLD1 cells with WT or mutated KRAS upon AMPK activation were investigated. In addition, xenograft tumor models with the nude mouse using DLD1 cells with WT or mutated KRAS were established to examine the effects of AMPK activation on KRAS mutation-mediated anti-EGFR antibody resistance.

Results

Higher levels of AMPK activity in CRC cells with wild-type KRAS treated with anti-EGFR antibody resulted in apoptosis induction. In contrast, CRC cells with mutated KRAS showed lower AMP-activated protein kinase (AMPK) activity and decreased sensitivity to the inhibitory effect of anti-EGFR antibody. CRC cells with mutated KRAS showed high levels of glycolysis and produced an excessive amount of ATP, which suppressed AMPK activation. The knockdown of AMPK expression in CRC cells with WT KRAS produced similar effects to those observed in cells with mutated KRAS and decreased their sensitivity to cetuximab. On the contrary, the activation of AMPK by metformin (Met) or 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR) could overcome the KRAS-induced resistance to the anti-EGFR antibody in vivo and in vitro. The activation of AMPK resulted in the inhibition of myeloid cell leukemia 1 (Mcl-1) translation through the suppression of the mammalian target of rapamycin (mTOR) pathway.

Conclusion

The results established herein indicate that targeting AMPK is a potentially promising and effective CRC treatment strategy.
Local preferences for three indigenous oil-seed plants and attitudes towards their conservation in the Kénédougou province of Burkina Faso, West-Africa
Authors: Tiétiambou Fanta Reine Sheirita , Salako Kolawolé Valère , Tohoun Jésukpégo Roméo , Ouédraogo Amadé
Published: July 2020

Background

Carapa procera,Lophira lanceolata, andPentadesma butyraceaare three underutilized but increasingly threatened indigenous oil-seed tree species (IOS) in tropical Africa. Because local knowledge is vital for sustainable management, this study investigated the socio-economic factors that explain local people’s (i) preferences for these IOS, (ii) attitudes toward their conservation, and (iii) ability to identify “plus trees” based on seed traits. We predicted a positive relationship between response variables and informants’ age, residence status, gender (femaleness), and existence of market opportunities for each IOS. We also predicted that a higher preference for a given IOS has a positive effect on people’s attitudes for its conservation and the aptitude to identify its “plus trees.” We additionally expected significant differences among ethnic groups for each response variable.

Methods

Data were collected through individual semi-structured interviews with 336 informants from 14 randomly selected villages in the species distribution area of Kénédougou province. For each species, the collected data were the number of actual uses reported (converted to use value—UV, as a measure of the species preference), practiced conservation actions (converted to conservation attitude using a four-scale scoring method), and possible criteria for selecting preferred trees for seed oil extraction. Generalized linear mixed models were used to test for the fixed effects of socio-economic factors, and account for the random variation across villages.

Results

The results showed species-specific patterns.Carapa procerahad the highest UV and hence was the most preferred IOS, particularly by women. Informants from the Siamou ethnic group had the highest UV irrespective of IOS. The most cited conservation actions were assisted natural regeneration and banning of tree cutting, which were practiced forC. proceraandL. lanceolata. No conservation measure was cited forP. butyracea. The practice of tree planting was not recorded for any of the IOS. Young and male informants participated less in conservation actions. Tree selection for oil-seed collection was mainly guided not by “oil extraction yield” but rather by the “quality of extracted oil” (namely oil color and taste for food uses, and oil bitterness for medicinal efficacy). The selection mainly concernedL. lanceolataand was mostly practiced by elderly people.

Conclusion

This study provided useful local knowledge-based information to guide conservation actions and valorization strategies of three IOS. The study sheds further light on the socio-economic factors that are associated to local people’s preferences, conservation attitudes, and individual tree selection.
Astaxanthin alleviates spinal cord ischemia-reperfusion injury via activation of PI3K/Akt/GSK-3β pathway in rats
Authors: Fu Jian , Sun Haibin , Wei Haofei , Dong Mingjie , Zhang Yongzhe , Xu Wei , Fang Yanwei , Zhao Jianhui
Published: July 2020

Background

Ischemia-reperfusion injury of the spinal cord (SCII) often leads to unalterable neurological deficits, which may be associated with apoptosis induced by oxidative stress and inflammation. Astaxanthin (AST) is a strong antioxidant and anti-inflammatory agent with multitarget neuroprotective effects. This study aimed to investigate the potential therapeutic effects of AST for SCII and the molecular mechanism.

Methods

Rat models of SCII with abdominal aortic occlusion for 40 min were carried out to investigate the effects of AST on the recovery of SCII. Tarlov’s scores were used to assess the neuronal function; HE and TUNEL staining were used to observe the pathological morphology of lesions. Neuron oxidative stress and inflammation were measured using commercial detection kits. Flow cytometry was conducted to assess the mitochondrial swelling degree. Besides, Western blot assay was used to detect the expression of PI3K/Akt/GSK-3β pathway-related proteins, as well as NOX2 and NLRP3 proteins.

Results

The results demonstrated that AST pretreatment promoted the hind limb motor function recovery and alleviated the pathological damage induced by SCII. Moreover, AST significantly enhanced the antioxidative stress response and attenuated mitochondrial swelling. However, AST pretreatment hardly inhibited the levels of proinflammatory cytokines after SCII. Most importantly, AST activated p-Akt and p-GSK-3β expression levels. Meanwhile, cotreatment with LY294002 (a PI3K inhibitor) was found to abolish the above protective effects observed with the AST pretreatment.

Conclusion

Overall, these results suggest that AST pretreatment not only mitigates pathological tissue damage but also effectively improves neural functional recovery following SCII, primarily by alleviating oxidative stress but not inhibiting inflammation. A possible underlying molecular mechanism of AST may be mainly attributed to the activation of PI3K/Akt/GSK-3β pathway.
Penetrating lung injury during Nuss procedure for pectus excavatum
Authors: Kim Do Yeon , Jeong Jin Yong
Published: July 2020

Life-threatening complications including cardiac perforation by the clamp or pectus bar during Nuss procedure have rarely been occurred. A rare case of lung entrapment between the pectus bar and chest wall after Nuss procedure was also reported. Thoracoscopy allows for direct visualization of the operative field, which prevents or promptly perceive these intrathoracic organ injuries. Recently, we encountered a case of penetrating lung injury during the Nuss procedure for pectus excavatum. And we agree with Mennie et al. who concluded thoracoscopic vision during Nuss procedure reduces the risk of major complication. In addition, we would like to emphasize to keep in mind what to check for routines with thoracoscopy during Nuss procedure.
COnsensus on Pediatric Pain in the Emergency Room: the COPPER project, issued by 17 Italian scientific societies
Authors: Benini Franca , Corsini Ilaria , Castagno Emanuele , Silvagni Davide , Lucarelli Annunziata , Giacomelli Luca , Amigoni Angela , Ancora Gina , Astuto Marinella , Borrometi Fabio , Casilli Rosa Maria , Chiappini Elena , Cutrera Renato , De Matteis Arianna , di Mauro Giuseppe , Musolino Anna , Fabbri Andrea , Ferrero Federica , Fornaro Martina , Gangemi Michele , Lago Paola , Macrì Francesco , Manfredini Luca , Memo Luigi , Minicucci Annamaria , Petralia Paolo , Pinelli Nicola , Antonucci Roberto , Tajè Silvia , Tizi Emiliano , Venturelli Leo , Zampogna Stefania , Urbino Antonio F.
Published: July 2020

In the pediatric setting, management of pain in the emergency department – and even in common care – is a challenging exercise, due to the complexity of the pediatric patient, poor specific training of many physicians, and scant resources.

A joint effort of several Italian societies involved in pediatrics or in pain management has led to the definition of the PIPER group and the COPPER project. By applying a modified Delphi method, the COPPER project resulted in the definition of 10 fundamental statements. These may represent the basis for improving the correct management of children pain in the emergency department.
Community Tele-pal: A community-developed, culturally based palliative care tele-consult randomized controlled trial for African American and White Rural southern elders with a life-limiting illness
Authors: Watts Kristen Allen , Gazaway Shena , Malone Emily , Elk Ronit , Tucker Rodney , McCammon Susan , Goldhagen Michele , Graham Jacob , Tassin Veronica , Hauser Joshua , Rhoades Sidney , Kagawa-Singer Marjorie , Wallace Eric , McElligott James , Kennedy Richard , Bakitas Marie
Published: July 2020

Background

Patients living in rural areas experience a variety of unmet needs that result in healthcare disparities. The triple threat of rural geography, racial inequities, and older age hinders access to high-quality palliative care (PC) for a significant proportion of Americans. Rural patients with life-limiting illness are at risk of not receiving appropriate palliative care due to a limited specialty workforce, long distances to treatment centers, and limited PC clinical expertise. Although culture strongly influences people’s response to diagnosis, illness, and treatment preferences, culturally based care models are not currently available for most seriously ill rural patients and their family caregivers. The purpose of this randomized clinical trial (RCT) is to compare a culturally based tele-consult program (that was developed by and for the rural southern African American (AA) and White (W) population) to usual hospital care to determine the impact on symptom burden (primary outcome) and patient and care partner quality of life (QOL), care partner burden, and resource use post-discharge (secondary outcomes) in hospitalized AA and White older adults with a life-limiting illness.

Methods

Community Tele-pal is a three-site RCT that will test the efficacy of a community-developed, culturally based PC tele-consult program for hospitalized rural AA and W older adults with life-limiting illnesses (n = 352) and a care partner. Half of the participants (n = 176) and a care partner (n = 176) will be randomized to receive the culturally based palliative care consult. The other half of the patient participants (n = 176) and care partners (n = 176) will receive usual hospital care appropriate to their illness.

Discussion

This is the first community-developed, culturally based PC tele-consult program for rural southern AA and W populations. If effective, the tele-consult palliative program and methods will serve as a model for future culturally based PC programs that can reduce patients’ symptoms and care partner burden.

Trial registration

ClinicalTrials.gov NCT03767517. Registered on 27 December 2018.
Consistency of trial reporting between ClinicalTrials.gov and corresponding publications: one decade after FDAAA
Authors: Talebi Ramtin , Redberg Rita F. , Ross Joseph S.
Published: July 2020

The FDA Amendments Act (FDAAA) required that information for certain clinical trials, such as details about study design features and endpoints, as well as results, be publicly reported in ClinicalTrials.gov. We conducted a cross-sectional analysis of phase III trials with primary results published between January 1, 2016, and June 30, 2017, in high-impact journals and found 74% contained at least one discrepancy between results reported in ClinicalTrials.gov and the corresponding publication. Our findings underscore the necessity for monitoring of clinical trial information and result reporting between sources; a checklist may provide a systemized procedure for investigators and editors to monitor accurate reporting.
Reconstruction of nonlinear integral inequalities associated with time scales calculus
Authors: Khan Zareen A.
Published: July 2020

In this paper, we build up some generalizations of nonlinear integral inequalities and recreate the results of some Pachpatte’s inequalities on time scales. We not just settle new estimated bounds of a particular class of nonlinear retarded dynamic inequalities, but additionally determine and unify continuous analogs alongside a subjective time scale $\mathbb{T}$
T
. We demonstrate applications of the treated inequalities to reflect the benefits of our work. The key effects will be proven by using the analysis procedure and the standard time-scale comparison theorem technique.
Participatory agenda setting as a process — of people, ambassadors and translation: a case study of participatory agenda setting in rural areas
Authors: Schroth Fabian , Glatte Hannah , Kaiser Simone , Heidingsfelder Marie
Published: July 2020

This paper presents a case study of a participatory agenda setting process in rural areas, with the aim of establishing at which points participation was achieved and via which channels and processes the results of said participation were introduced into local and overarching policy agendas. We argue that participatory agenda setting involves two central challenges, namely the development of dialogue formats and procedures that enable members of the public to take part in the process, and the selection and use of the appropriate channels for conveying their input to the relevant decision-makers. Agenda setting is thus a process during which concepts and issues are collaboratively uncovered or developed and then integrated, via networks, into policy and research strategy. Accordingly, this process encompasses the actors involved in the agenda setting process, the procedures that make participation possible, and the channels via which the results are then transferred.
Density deconvolution for generalized skew-symmetric distributions
Authors: Potgieter Cornelis J.
Published: July 2020

The density deconvolution problem is considered for random variables assumed to belong to the generalized skew-symmetric (GSS) family of distributions. The approach is semiparametric in that the symmetric component of the GSS distribution is assumed known, and the skewing function capturing deviation from the symmetric component is estimated using a deconvolution kernel approach. This requires the specification of a bandwidth parameter. The mean integrated square error (MISE) of the GSS deconvolution estimator is derived, and two bandwidth estimation methods based on approximating the MISE are also proposed. A generalized method of moments approach is also developed for estimation of the underlying GSS location and scale parameters. Simulation study results are presented including a comparing the GSS approach to the nonparametric deconvolution estimator. For most simulation settings considered, the GSS estimator is seen to have performance superior to the nonparametric estimator.
Prognosis of pathogen-proven acute respiratory distress syndrome diagnosed from a protocol that includes bronchoalveolar lavage: a retrospective observational study
Authors: Kyo Michihito , Hosokawa Koji , Ohshimo Shinichiro , Kida Yoshiko , Tanabe Yuko , Shime Nobuaki
Published: July 2020

Background

To treat patients with acute respiratory distress syndrome (ARDS), it is important to diagnose specific lung diseases and identify common risk factors. Our facility focuses on using bronchoalveolar lavage (BAL) to identify precise risk factors and determine the causative pathogen of ARDS within 24 h of intensive care unit (ICU) admission. This study evaluated the prognoses of pathogen-proven ARDS patients who were diagnosed or identified with risk factors using a diagnostic protocol, which included BAL, compared with the prognoses of pathogen-unproven ARDS patients.

Methods

This retrospective observational study was conducted in the ICU at a tertiary hospital from October 2015 to January 2019. We enrolled patients with respiratory distress who were on mechanical ventilation for more than 24 h in the ICU and who were subjected to our diagnostic protocol. We compared the disease characteristics and mortality rates between pathogen-proven and pathogen-unproven ARDS patients.

Results

Seventy ARDS patients were included, of whom, 50 (71%) had pathogen-proven ARDS as per our protocol. Mortality rates in both the ICU and the hospital were significantly lower among pathogen-proven ARDS patients than among pathogen-unproven ARDS patients (10% vs. 50%, p = 0.0006; 18% vs. 55%, p = 0.0038, respectively). Pathogen-proven ARDS patients were independently associated with hospital survival (adjusted hazard ratio, 0.238; 95% confidence interval, 0.096–0.587; p = 0.0021).

Conclusions

Our diagnostic protocol, which included early initiation of BAL, enabled diagnosing pathogen-proven ARDS in 71% of ARDS patients. These patients were significantly associated with higher hospital survival rates. The diagnostic accuracy of our diagnostic protocol, which includes BAL, remains unclear.
Author’s response to letter “Antimicrobials administration time in patients with suspected sepsis: faster is better for severe patients”
Authors: Ascuntar Johana , Mendoza Deibie , Jaimes Fabián
Published: July 2020

We are appreciative to Dr. Jouffroy and Pr. Vivien for their responses and insights, and we agree with their words about the controversial aspect timing to antibiotic administration. Nevertheless, we stand firmly that it is not just about the time of administration of antimicrobials, but the early recognition and the comprehensive approach to recognize the most severe patients.
Causal assessment in demographic research
Authors: Wunsch Guillaume , Gourbin Catherine
Published: July 2020

Causation underlies both research and policy interventions. Causal inference in demography is however far from easy, and few causal claims are probably sustainable in this field. This paper targets the assessment of causality in demographic research. It aims to give an overview of the methodology of causal research, pointing out various problems that can occur in practice. The “Intervention studies” section critically examines the so-called gold standard in causality assessment in experimental studies, randomized controlled trials, and the use of quasi-experiments and interventions in observational studies. The “Multivariate statistical models” section deals with multivariate statistical models linking a mortality or fertility indicator to a series of possible causes and controls. Single and multiple equation models are considered. The “Mechanisms and structural causal modelling” section takes into account a more recent trend, i.e., mechanistic explanations in causal research, and develops a structural causal modelling framework stemming from the pioneering work of the Cowles Commission in econometrics and of Sewall Wright in population genetics. The “Assessing causality in demographic research” section examines how causal analysis could be further applied in demographic studies, and a series of proposals are discussed for this purpose. The paper ends with a conclusion pointing out, in particular, the relevance of structural equation models, of triangulation, and of systematic reviews for causal assessment.
Intensive care unit (ICU) diaries and the experiences of patients’ families: a grounded theory approach in a lower middle-income country (LMIC)
Authors: Tripathy Swagata , Acharya Swati Priyadarshini , Sahoo Alok Kumar , Mitra Jayanta Kumar , Goel Kishen , Ahmad Suma Rabab , Hansdah Upendra
Published: July 2020

Objective

An intensive care unit (ICU) diary is a relatively new concept in low middle-income countries (LMICs). Illiteracy and socio-cultural inhibitions may affect the use and utility of this intervention, which has proven beneficial to patients and their families in high income countries (HICs). We aimed to explore how families of ICU patients experienced ICU diaries in our set up by using the Grounded Theory (GT) approach. A relatively new research tool, this enables exploration of a phenomenon to build theories in areas hitherto uncharted.

Method

A clinical psychologist did 29 in-depth interviews of relatives of 13 patients admitted in the ICU for > 24 h for whom an ICU diary was being maintained. We used a three-step coding process- open, axial, and selective coding, followed by the formulation of a theory embedded in the data.

Results

We found that the younger relatives of ICU patients accepted the idea better (age 30, SD 6) Half (48%) had education between 5th to 10th standards. Emergent themes suggested that for the family members, reading and writing the diary brought novelty, acted as a communication enabler, spiritual truss, and improved knowledge leading to change in perspective about the health care system. It also became a bridge to community bonding after patient discharge. Starting with appreciating the novelty of ‘diary entries,’ which was a new and exciting concept, family members used the diaries to communicate with health care workers (to gain information and understanding about the disease and treatment) and the patient to express their love and to maintain a connection. The diary acted as a confessional for hopes, fears, guilt, and faith for many members. As a tool, it enabled them to understand medical personnel as human beings and to appreciate their efforts, effectively improving confidence in the system. Finally, upon returning home, the diary was a crowd puller for extended family and neighbors encouraging discussions and enhancing bonding and information sharing.

Conclusions

Our findings indicate a good acceptance of ICU diaries by family members in our ICU. With less literate, admitted ‘shy ‘members, in a society where ‘diary writing’ is not culturally rampant, the appreciation for the novel concept was universal. We see a place for these interventions not only at the patient/ family level but also as a means to ‘correct’ the image of health care workers in our society by humanizing ourselves to the end-user- the patient and his family.