bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pharmacologically induced weight loss is associated with distinct gut microbiome changes in obese rats
Authors: Raineri Silvia , Sherriff Julia A. , Thompson Kevin S. J. , Jones Huw , Pfluger Paul T. , Ilott Nicholas E. , Mellor Jane 
Published: April 2022

Abstract
Background
Obesity, metabolic disease and some psychiatric conditions are associated with changes to relative abundance of bacterial species and specific genes in the faecal microbiome. Little is known about the impact of pharmacologically induced weight loss on distinct microbiome species and their respective gene programs in obese individuals.

Methodology
Using shotgun metagenomics, the composition of the microbiome was obtained for two cohorts of obese female Wistar rats (n = 10–12, total of 82) maintained on a high fat diet before and after a 42-day treatment with a panel of four investigatory or approved anti-obesity drugs (tacrolimus/FK506, bupropion, naltrexone and sibutramine), alone or in combination.

Results
Only sibutramine treatment induced consistent weight loss and improved glycaemic control in the obese rats. Weight loss was associated with reduced food intake and changes to the faecal microbiome in multiple microbial taxa, genes, and pathways. These include increased β-diversity, increased relative abundance of multiple Bacteroides species, increased Bacteroides/Firmicutes ratio and changes to abundance of genes and species associated with obesity-induced inflammation, particularly those encoding components of the flagellum and its assembly.

Conclusions
Sibutramine-induced weight loss in obese rats is associated with improved metabolic health, and changes to the faecal microbiome consistent with a reduction in obesity-induced bacterially-driven inflammation.
Analysis of endophyte diversity of two Gentiana plants species and the association with secondary metabolite
Authors: Hou Qin Zheng , Chen Da Wei , Wang Yu Pei , Ehmet Nurbiye , Ma Jing , Sun Kun 
Published: April 2022

Abstract
Background
The influence of external environmental factors on secondary metabolites of medicinal plants has always been studied. However, little is known about the relationships between endophytes and host metabolites, especially the relationship differences between different plant species. Thus, we used high-throughput sequencing methods to compare endophyte diversity from roots of two closely related species, Gentiana officinalis and G. siphonantha, from the same production area, and analyze the association with four secondary metabolites (Gentiopicroside, Loganic acid, Swertiamarine and Sweroside).

Results
The fungal and bacteria communities’ richness and diversity of G. siphonantha was higher than G. officinalis. Ascomycota and Proteobacteria were dominant fungal and bacterial phylum of the two closely related species. At the genus level, Tetracladium and Cadophora were dominant fungal genus in G. officinalis and G. siphonantha samples, respectively. While Pseudomonas was dominant bacterial genus in two closely related species, with relative abundances were 8.29 and 8.05%, respectively. Spearman analysis showed that the content of loganic acid was significantly positively correlated with endophytic fungi, the content of gentiopicroside, swertiamarine and sweroside were significantly positively correlated with endophytic bacteria in the two related species. PICRUSt and FUNGuild predictive analysis indicated that metabolism and saprotroph was primary function of endophytic bacteria and fungi in the two related species.

Conclusion
Our results will expand the knowledge on relationships of plant-microbe interactions and offer pivotal information to reveal the role of endophytes in the production of Gentiana plant and its important secondary metabolite.
The Gastrodia menghaiensis (Orchidaceae) genome provides new insights of orchid mycorrhizal interactions
Authors: Jiang Yan , Hu Xiaodi , Yuan Yuan , Guo Xuelian , Chase Mark W. , Ge Song , Li Jianwu , Fu Jinlong , Li Kui , Hao Meng , Wang Yiming , Jiao Yuannian , Jiang Wenkai , Jin Xiaohua 
Published: April 2022

Abstract
Background
To illustrate the molecular mechanism of mycoheterotrophic interactions between orchids and fungi, we assembled chromosome-level reference genome of Gastrodia menghaiensis (Orchidaceae) and analyzed the genomes of two species of Gastrodia.

Results
Our analyses indicated that the genomes of Gastrodia are globally diminished in comparison to autotrophic orchids, even compared to Cuscuta (a plant parasite). Genes involved in arbuscular mycorrhizae colonization were found in genomes of Gastrodia, and many of the genes involved biological interaction between Gatrodia and symbiotic microbionts are more numerous than in photosynthetic orchids. The highly expressed genes for fatty acid and ammonium root transporters suggest that fungi receive material from orchids, although most raw materials flow from the fungi. Many nuclear genes (e.g. biosynthesis of aromatic amino acid L-tryptophan) supporting plastid functions are expanded compared to photosynthetic orchids, an indication of the importance of plastids even in totally mycoheterotrophic species.

Conclusion
Gastrodia menghaiensis has the smallest proteome thus far among angiosperms. Many of the genes involved biological interaction between Gatrodia and symbiotic microbionts are more numerous than in photosynthetic orchids.
Adherence of physicians to evidence-based management guidelines for treating type 2 diabetes and atherosclerotic cardiovascular disease in Ajman, United Arab Emirates
Authors: Alliabi Farah Jabbar Ali , Jaber Ammar Ali Saleh , Jallo Mahir Khalil Ibrahim , Baig Mirza R. 
Published: April 2022

Abstract
Background
Good adherence by physicians to treatment guidelines for type II diabetes mellitus (T2DM) could improve therapy outcome for patients. In this retrospective, cross-sectional study, we assessed physicians’ adherence to evidence-based guidelines for T2DM management in adult patients (aged ≥18 years) with either confirmed atherosclerotic cardiovascular disease (ASCVD) or those at high risk of developing ASCVD at the Thumbay Academic Health Center, United Arab Emirates (UAE).

Methods
Relevant data was obtained from patients’ medical records, assessed, and compared based on the 2018 diabetes guidelines of the American Diabetes Association and European Association for the Study of Diabetes.

Results
A total of 218 patients (186 males and 32 females) were included in the analysis. Of these, 122 were prescribed either sodium-glucose co-transporter-2(SGLT2) inhibitors or glucagon-like peptide 1 (GLP-1) receptor agonists and 34 were prescribed both. The overall adherence to the guidelines was 56%, which was significantly influenced by body mass index (BMI), hemoglobin A1c (HbA1c) levels, and estimated average glucose (eAG).

Conclusions
Adherence to guidelines was significantly high when treating patients with elevated levels of HbA1c and eAG, suggesting that physicians are more likely to prescribe SGLT2 inhibitors or/and GLP-1 receptor agonists to such patients. Physicians’ adherence to guidelines was significantly correlated with patients’ BMI and the levels of HbA1c and eAG. To the best of our knowledge, this is the first study conducted on diabetes and its risk factors in UAE.
The impact of intravenous iron supplementation in elderly patients undergoing major surgery
Authors: Blum Lea Valeska , Zierentz Philipp , Hof Lotta , Kloka Jan Andreas , Messroghli Leila , Zacharowski Kai , Meybohm Patrick , Choorapoikayil Suma 
Published: April 2022

Abstract
Background
Age and preoperative anaemia are risk factors for poor surgical outcome and blood transfusion. The aim of this study was to examine the effect of iron supplementation in iron-deficient (ID) elderly patients undergoing major surgery.

Method
In this single-centre observational study, patients ≥ 65 years undergoing major surgery were screened for anaemia and ID. Patients were assigned to the following groups: A− (no anaemia); A−,ID+,T+ (no anaemia, iron-deficient, intravenous iron supplementation); A+ (anaemia); and A+,ID+,T+ (anaemia, iron-deficient, intravenous iron supplementation).

Results
Of 4,381 patients screened at the anaemia walk-in clinic, 2,381 (54%) patients were ≥ 65 years old and 2,191 cases were included in analysis. The ID prevalence was 63% in patients with haemoglobin (Hb) < 8 g/dl, 47.2% in patients with Hb from 8.0 to 8.9 g/dl, and 44.3% in patients with Hb from 9 to 9.9 g/dl. In severely anaemic patients, an Hb increase of 0.6 (0.4; 1.2) and 1.2 (0.7; 1.6) g/dl was detected with iron supplementation 6–10 and > 10 days before surgery, respectively. Hb increased by 0 (-0.1; 0) g/dl with iron supplementation 1–5 days before surgery, 0.2 (-0.1; 0.5) g/dl with iron supplementation 6–10 days before surgery, and 0.2 (-0.2; 1.1) g/dl with supplementation > 10 days before surgery (p < 0.001 for 1–5 vs. 6–10 days). Overall, 58% of A+,ID+,T+ patients showed an Hb increase of > 0.5 g/dl. The number of transfused red blood cell units was significantly lower in patients supplemented with iron (0 (0; 3)) compared to non-treated anaemic patients (1 (0; 4)) (p = 0.03). Patients with iron supplementation > 6 days before surgery achieved mobility 2 days earlier than patients with iron supplementation < 6 days.

Conclusions
Intravenous iron supplementation increases Hb level and thereby reduces blood transfusion rate in elderly surgical patients with ID anaemia.
Interaction between ω-6 fatty acids intake and blood cadmium on the risk of low cognitive performance in older adults from National Health and Nutrition Examination Survey (NHANES) 2011–2014
Authors: Huang Guangxiang , Ren Gang 
Published: April 2022

Abstract
Background
Identifying preventable diets and environmental exposure is essential to ensuring the health of the aging population. This study evaluated the interaction effect between blood cadmium and ω-6 fatty acids intake on low cognitive performance in Americans.

Method
The data of this cross-sectional study were obtained from the 2011–2012 and 2013–2014 National Health and Nutritional Examination Survey (NHANES). Cognitive performance was measured by the Consortium to Establish a Registry for Alzheimer’s Disease test, Animal Fluency Test, and Digit Symbol Substitution Test. Multivariate logistic regression models were used.

Results
A total of 1,918 individuals were included, with 467 (24.35%) low cognitive performance. Compared with participants with normal-level blood cadmium, those with high-level blood cadmium had a higher risk of low cognitive performance [odds ratio (OR) was 1.558 with 95% confidence interval (CI): 1.144–2.123]. Low-level ω-6 fatty acids intake was positively associated with low cognitive performance [OR = 1.633 (95%CI: 1.094–2.436)] compared with normal-level intake. Moreover, there was a significant interaction between low-level ω-6 fatty acids intake and high-level blood cadmium on the risk of low cognitive performance (relative excess risk due to interaction: 0.570, 95%CI: 0.208-0.932; the attributable proportion of interaction: 0.219, 95%CI: 0.102‐0.336; synergy index: 1.552, 95%CI: 1.189‐2.027).

Conclusions
There was a synergistic interaction between low-level ω-6 fatty acids intake and high-level blood cadmium on low cognitive performance. Low-level ω-6 fatty acids intake may amplify the adverse effects of long-term exposure to cadmium on cognitive performance. This may have a certain significance for the prevention of cognitive decline in the elderly.
Incidence and factors associated with active tuberculosis among people living with HIV after long-term antiretroviral therapy in Thailand: a competing risk model
Authors: Gatechompol Sivaporn , Sophonphan Jiratchaya , Ubolyam Sasiwimol , Avihingsanon Anchalee , van Leth Frank , Cobelens Frank , Kerr Stephen J. 
Published: April 2022

Abstract
Background
Antiretroviral therapy (ART) is known to reduce tuberculosis (TB) incidence among people living with HIV (PLWH). However, studies describing the impact of long-term ART and CD4 count recovery on TB incidence remain scarce due to limited follow up in previous studies. We evaluated TB incidence in a long-term cohort of PLWH on ART in Thailand.

Methods
We conducted an analysis of PLWH aged ≥ 18 years who started ART between 1996 and December 2020. Participants were followed up every 6 months for routine HIV care. TB risk factors, body mass index (BMI), physical examination and full differential blood counts were evaluated at each clinic visit, and CD4 cell counts and HIV RNA every 12 months. Participants diagnosed with TB > 3 months after starting ART were classified as incident cases. Time to event models with death as a competing risk, were used to derive the TB cumulative incidence function (CIF) after ART initiation, and assess time-updated factors associated with incident TB using a six month lag.

Results
A total of 2,636 PLWH contributing 24,229 person years (PY) of follow-up on ART were analysed. Median age was 32.0 (IQR 27.4–37.6) years; 67.5% were male. Median CD4 cell count at ART initiation was 264 (IQR 167–379) cells/mm3 and median follow-up duration was 7.6 (IQR 1.9–15.7) years. During follow-up, 113 PLWH developed TB. The probability of incident TB was 0.7%, 1.7%, 3.3% and 4.3%, at 1, 2, 5 and 7 years after ART initiation, respectively. TB CIF was highest among participants with CD4 < 50 cells/mm3. The overall crude incidence of TB was 4.66 (95% CI 3.87–5.60) per 1000 PY. Low CD4 count, BMI < 18 kg/m2, and substance use in the previous six months were significantly associated with incident TB. Incidence declined with time on suppressive ART, but remained higher than the Thai general population 7 years after ART initiation (2.2 vs 1.5/1000 PY, respectively).

Conclusion
Despite a marked reduction in TB incidence following ART, ongoing TB risk remains high among PLWH, despite long-term suppressive ART. Those with low CD4 cell counts, who are underweight, or currently having substance abuse should be carefully monitored.
Comparative study on efficacy and safety of ultrasound guided transoral and transcutaneous core needle biopsy in patients with oral masses
Authors: Wei Ting , Lu Man , Li Juan , Hu Ziyue , Li Tingting , Cheng Xueqing , Wang Lu , Pu Wei 
Published: April 2022

Abstract
Background
Ultrasound (US) guided transoral biopsy is a novel and safe procedure for obtaining tissue in patients with oral masses. However, this procedure is less commonly used in comparison to US guided transcutaneous biopsy. The aim of this study is to compare the efficacy and safety of US-guided transoral and transcutaneous core needle biopsy (CNB) in patients with oral masses.

Methods
From November 2019 to March 2021, consecutive patients with oral masses were randomly assigned to undergo US-guided transoral CNB (transoral group) and US-guided transcutaneous CNB from a submental approach (transcutaneous group). During the operation, procedure time, intra‑operative blood loss volume, diagnostic performance, rate of complications and pain level were recorded and compared.

Results
There were 112 patients (62 in the transoral group and 50 in the transcutaneous group) evaluated in this study. The postprocedural complication rate of the transcutaneous group was significantly higher than the transoral group (24% vs. 0%, P = 0.000). There was no significant difference in accuracy (95.2% vs. 88%, P = 0.30), biopsy time (76 ± 12 s vs. 80 ± 13 s, p = 0.09), blood losses (2.6 ± 0.5 mL vs. 2.7 ± 0.4 mL, p = 0.17) and visual analogue score (p = 0.327 and p = 0.444 before and after the sampling procedure) between the two groups.

Conclusion
US-guided transoral CNB results in high rates of technical success and lower rates of postprocedural complications.
Longitudinal profiling of circulating tumour DNA for tracking tumour dynamics in pancreatic cancer
Authors: Sivapalan Lavanya , Thorn Graeme J. , Gadaleta Emanuela , Kocher Hemant M. , Ross-Adams Helen , Chelala Claude 
Published: April 2022

Abstract
Background
The utility of circulating tumour DNA (ctDNA) for longitudinal tumour monitoring in pancreatic ductal adenocarcinoma (PDAC) has not been explored beyond mutations in the KRAS proto-oncogene. Here, we aimed to characterise and track patient-specific somatic ctDNA variants, to assess longitudinal changes in disease burden and explore the landscape of actionable alterations.

Methods
We followed 3 patients with resectable disease and 4 patients with unresectable disease, including 4 patients with ≥ 3 serial follow-up samples, of whom 2 were rare long survivors (> 5 years). We performed whole exome sequencing of tumour gDNA and plasma ctDNA (n = 20) collected over a ~ 2-year period from diagnosis through treatment to death or final follow-up. Plasma from 3 chronic pancreatitis cases was used as a comparison for analysis of ctDNA mutations.

Results
We detected > 55% concordance between somatic mutations in tumour tissues and matched serial plasma. Mutations in ctDNA were detected within known PDAC driver genes (KRAS, TP53, SMAD4, CDKN2A), in addition to patient-specific variants within alternative cancer drivers (NRAS, HRAS, MTOR, ERBB2, EGFR, PBRM1), with a trend towards higher overall mutation loads in advanced disease. ctDNA alterations with potential for therapeutic actionability were identified in all 7 patients, including DNA damage response (DDR) variants co-occurring with hypermutation signatures predictive of response to platinum chemotherapy. Longitudinal tracking in 4 patients with follow-up > 2 years demonstrated that ctDNA mutant allele fractions and clonal trends were consistent with CA19-9 measurements and/or clinically reported disease burden. The estimated prevalence of ‘stem clones’ was highest in an unresectable patient where changes in ctDNA dynamics preceded CA19-9 levels. Longitudinal evolutionary trajectories revealed ongoing subclonal evolution following chemotherapy.

Conclusion
These results provide proof-of-concept for the use of exome sequencing of serial plasma to characterise patient-specific ctDNA profiles, and demonstrate the sensitivity of ctDNA in monitoring disease burden in PDAC even in unresectable cases without matched tumour genotyping. They reveal the value of tracking clonal evolution in serial ctDNA to monitor treatment response, establishing the potential of applied precision medicine to guide stratified care by identifying and evaluating actionable opportunities for intervention aimed at optimising patient outcomes for an otherwise intractable disease.
Pain management after third molar extractions in adolescents: a qualitative study
Authors: Mitchell Shannon Gwin , Truitt Anjali R. , Davin Lauryn M. , Rindal D. Brad 
Published: April 2022

Abstract
Background
Understanding how adolescent patients make decisions about pain management after complex dental procedures could help reduce the use of opioid medications and the potential for future opioid misuse in this population. This qualitative study explores how adolescents manage pain, including how decision making with parents and providers affect their experience with opioid and non-opioid analgesics after third molar dental extractions.

Methods
We used a qualitative approach for the analysis of 30 telephone-based semi-structured interviews completed by 15 dyads between May and August 2019, which included 15 adolescents (15–17 years) who underwent a dental extraction, and a parent or guardian for each adolescent. The total sample included 30 participants. Interviews were conducted separately for patients and parents. De-identified interview transcripts were analyzed using qualitative analysis software using a directed content analysis approach.

Results
A total of 15 patient/parent dyads were interviewed. Key themes associated with pain management included sources of information, pain management behaviors engaged in by the adolescents and their caregivers, and the use of medication. In addition to conversations with their dental provider, most patients and their parents discussed pain management plans that included non-medication options, over-the-counter medications, and opioid medications to be taken as needed, which guided their post-extraction behaviors. All participants reported that the adolescent received an opioid prescription for post-extraction pain management, to be taken on an “as needed” basis, but most only took it the day of the extraction and up to 2 days following, usually based on the patient’s reported pain levels and perceptions of over-the-counter medication adequacy. Participants said they did not receive guidance from their provider concerning disposal of unused opioid medications.

Conclusions
Involving adolescents in the pain management decision making process and allowing them to carry out the plan with some caregiver support was acceptable and well executed following third molar extractions. Providers may have an opportunity to reduce the number of opioids prescribed, since respondents reported little to no use of opioids that they were prescribed. Providers should educate patients and their parents about safe disposal of opioids to mitigate the potential for diversion.
Optimal timing and effectiveness of COVID-19 outbreak responses in China: a modelling study
Authors: Zhang Anthony Zhenhuan , Enns Eva A. 
Published: April 2022

Abstract
Background
In January 2020, an outbreak of atypical pneumonia caused by a novel coronavirus, SARS-CoV-2, was reported in Wuhan, China. On Jan 23, 2020, the Chinese government instituted mitigation strategies to control spread. Most modeling studies have focused on projecting epidemiological outcomes throughout the pandemic. However, the impact and optimal timing of different mitigation approaches have not been well-studied.

Methods
We developed a mathematical model reflecting SARS-CoV-2 transmission dynamics in an age-stratified population. The model simulates health and economic outcomes from Dec 1, 2019 through Mar 31, 2020 for cities including Wuhan, Chongqing, Beijing, and Shanghai in China. We considered differences in timing and duration of three mitigation strategies in the early phase of the epidemic: city-wide quarantine on Wuhan, travel history screening and isolation of travelers from Wuhan to other Chinese cities, and general social distancing.

Results
Our model estimated that implementing all three mitigation strategies one week earlier would have averted 35% of deaths in Wuhan (50% in other cities) with a 7% increase in economic impacts (16-18% in other cities). One week’s delay in mitigation strategy initiation was estimated to decrease economic cost by the same amount, but with 35% more deaths in Wuhan and more than 80% more deaths in the other cities. Of the three mitigation approaches, infections and deaths increased most rapidly if initiation of social distancing was delayed. Furthermore, social distancing of working-age adults was most critical to reducing COVID-19 outcomes versus social distancing among children and/or the elderly.

Conclusions
Optimizing the timing of epidemic mitigation strategies is paramount and involves weighing trade-offs between preventing infections and deaths and incurring immense economic impacts. City-wide quarantine was not as effective as city-wide social distancing due to its much higher daily cost than social distancing. Under typical economic evaluation standards, the optimal timing for the full set of control measures would have been much later than Jan 23, 2020 (status quo).