bluuebunny/crossref_metadata_2025_split huggingface dataset:
A proposal for a comprehensive approach to infections across the surgical pathway
Authors: Sartelli Massimo , Pagani Leonardo , Iannazzo Stefania , Moro Maria Luisa , Viale Pierluigi , Pan Angelo , Ansaloni Luca , Coccolini Federico , D’Errico Marcello Mario , Agreiter Iris , Amadio Nespola Giorgio , Barchiesi Francesco , Benigni Valeria , Binazzi Raffaella , Cappanera Stefano , Chiodera Alessandro , Cola Valentina , Corsi Daniela , Cortese Francesco , Crapis Massimo , Cristini Francesco , D’Arpino Alessandro , De Simone Belinda , Di Bella Stefano , Di Marzo Francesco , Donati Abele , Elisei Daniele , Fantoni Massimo , Ferrari Anna , Foghetti Domitilla , Francisci Daniela , Gattuso Gianni , Giacometti Andrea , Gesuelli Guido Cesare , Marmorale Cristina , Martini Enrica , Meledandri Marcello , Murri Rita , Padrini Daniela , Palmieri Dalia , Pauri Paola , Rebagliati Carla , Ricchizzi Enrico , Sambri Vittorio , Schimizzi Anna Maria , Siquini Walter , Scoccia Loredana , Scoppettuolo Giancarlo , Sganga Gabriele , Storti Nadia , Tavio Marcello , Toccafondi Giulio , Tumietto Fabio , Viaggi Bruno , Vivarelli Marco , Tranà Cristian , Raso Melina , Labricciosa Francesco Maria , Dhingra Sameer , Catena Fausto 
Published: February 2020

AbstractDespite evidence supporting the effectiveness of best practices in infection prevention and management, many healthcare workers fail to implement them and evidence-based practices tend to be underused in routine practice. Prevention and management of infections across the surgical pathway should always focus on collaboration among all healthcare workers sharing knowledge of best practices. To clarify key issues in the prevention and management of infections across the surgical pathway, a multidisciplinary task force of experts convened in Ancona, Italy, on May 31, 2019, for a national meeting. This document represents the executive summary of the final statements approved by the expert panel.
Gene polymorphisms and expression levels of interleukin-6 and interleukin-10 in lumbar disc disease: a meta-analysis and immunohistochemical study
Authors: Guan Yewen , Wang Siting , Wang Jiaqi , Meng Dihua , Wu Huihong , Wei Qingjun , Jiang Hua 
Published: February 2020

Abstract
Background
To investigate the association between interleukin-6 (IL-6) (rs1800795, rs1800796, rs1800797, rs13306435, rs2069849) and interleukin-10 (IL-10) (rs1800871, rs1800896) gene polymorphisms, expression levels, and lumbar disc disease (LDD).

Methods
We conducted a literature research on PubMed, Embase, Web of Science, Cochrane Library, and China National Knowledge Infrastructure (CNKI) until February 28, 2019. We included all case-control studies about the association between IL-6 and IL-10 gene polymorphisms and LDD. The odds ratio (OR) and 95% confidence interval (CI) were calculated to estimate the strength of association. Statistical analysis was conducted by Review Manager (RevMan) 5.3 software. Furthermore, immunohistochemistry (IHC) and RT-PCR were performed to evaluate IL-6 and IL-10 expressions in the normal and degenerated disc.

Results
A total of 6 studies, involving 1456 cases and 1611 controls, were included in this meta-analysis. G alleles of rs1800795 and rs1800797 in the IL-6 gene were significantly associated with LDD (rs1800795: G vs. C, OR = 1.38, 95% CI = 1.16–1.64, P = 0.0002; rs1800797: G vs. A, OR = 1.35, 95% CI = 1.14–1.61, P = 0.0006). Begg’s funnel plot and Egger’s tests did not show any evidence of publication bias. IL-6 expression and IL-6 mRNA levels were significantly increased in the degenerated disc compared with those in the normal disc (IL-6 immunopositive cells, 73.68 ± 10.99% vs. 37.23 ± 6.42%, P < 0.001).

Conclusions
IL-6 gene polymorphisms (rs1800795 and rs1800797) were significantly associated with susceptibility to LDD. A high expression level of IL-6 may be an important risk factor for LDD.
Recognizable neonatal clinical features of aplasia cutis congenita
Authors: Schierz Ingrid Anne Mandy , Giuffrè Mario , Del Vecchio Antonello , Antona Vincenzo , Corsello Giovanni , Piro Ettore 
Published: February 2020

Abstract
Background
Aplasia cutis congenita (ACC), classified in nine groups, is likely to be underreported, since milder isolated lesions in wellbeing newborns could often be undetected, and solitary lesions in the context of polymalformative syndromes could not always be reported. Regardless of form and cause, therapeutic options have in common the aim to restore the deficient mechanical and immunological cutaneous protection and to limit the risk of fluid leakage or rupture of the exposed organs. We aimed to review our institutional prevalence, comorbidities, treatment and outcome of newborns with ACC.

Methods
We conducted a retrospective study including all newborns affected by ACC and admitted at the University Mother-Child Department from October 2010 to October 2019. Anthropometric and clinical characteristics of ACC1 versus a non-isolated ACC group were analyzed.

Results
We encountered 37 newborns, 16 with ACC1 versus 21 with non-isolated ACC. The incidence rate of 0.1% in ACC1 was higher than expected, while 19% of cases showed intrafamilial autosomal dominant transmission. Higher birth weight centile, though lower than reference population, being adequate for gestational age, normal Apgar score and euglycemia characterizing ACC1 resulted associated to a rapid tissue regeneration. Non-isolated ACC, in relation to concomitant congenital anomalies and higher prematurity rate, showed more surgical and medical complications along with the risk of neonatal death. Specifically, newborns with ACC4 were characterized by the frequent necessity of abdominal wall defect repair, responsible for the occurrence of an abdominal compartment syndrome.

Conclusion
Prompt carefully assessment of the newborn with ACC in order to exclude concomitant other congenital malformations, provides clues to the underlying pathophysiology, and to the short-term prognosis. Family should be oriented toward identification of other family members affected by similar pathology, while obstetric history should exclude initial multiple pregnancy with death of a co-twin, placental anomalies and drug assumption. Molecular-genetic diagnosis and genetic counseling are integrative in individualized disease approach.
A randomised, multi-centre trial of total ankle replacement versus ankle arthrodesis in the treatment of patients with end stage ankle osteoarthritis (TARVA): statistical analysis plan
Authors:   on behalf of the TARVA Study Group, Muller Patrick , Skene Simon S. , Chowdhury Kashfia , Cro Suzie , Goldberg Andrew J. , Doré Caroline J. 
Published: February 2020

Abstract
Background
The total ankle replacement versus ankle arthrodesis (TARVA) trial aims to determine which surgical procedure confers the greatest improvement in pain-free function for patients with end-stage ankle osteoarthritis. Both procedures are effective but there has not yet been a direct comparison to establish which is superior. This article describes the statistical analysis plan for this trial as an update to the published protocol. It is written prior to the end of patient follow-up, while the outcome of the trial is still unknown.

Design and methods
TARVA is a randomised, un-blinded, parallel group trial of total ankle replacement versus ankle arthrodesis. The primary outcome is the Manchester-Oxford Foot Questionnaire walking/standing domain score at 52 weeks post-surgery. Secondary outcomes include measures of pain, social interaction, physical function, quality of life, and range of motion. We describe in detail the statistical aspects of TARVA: the outcome measures, the sample size calculation, general analysis principles including treatment of missing data, the planned descriptive statistics and statistical models, and planned subgroup and sensitivity analyses.

Discussion
The TARVA statistical analysis will provide comprehensive and precise information on the relative effectiveness of the two treatments. The plan will be implemented in January 2020 when follow-up for the trial is completed.

Trial registration
ISRCTN registry number 60672307, ClinicalTrials.gov registration number NCT02128555. Registered 1 May 2014. Recruitment started in January 2015 and ended in January 2019.
A randomized controlled trial investigating the effect of a diet low in fermentable oligosaccharides, disaccharides, monosaccharides, and polyols on the intestinal microbiome and inflammation in patients with ulcerative colitis: study protocol for a randomized controlled trial
Authors: Milajerdi Alireza , Sadeghi Omid , Siadat Seyed Davar , Keshavarz Seyed Ali , Sima Alireza , Vahedi Homayoon , Adibi Peyman , Esmaillzadeh Ahmad 
Published: February 2020

Abstract
Background
No conclusive treatment is available for irritable bowel disease (IBD). Adherence to a diet low in fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAPs) might alleviate clinical symptoms of IBD. However, no study has investigated the effect of low FODMAPs diet on the intestinal microbiota and inflammatory biomarkers in patients with IBD. The aim of current study is to examine the effect a low FODMAP diet on IBD symptoms, inflammation, and the intestinal microbiota in patients with ulcerative colitis.

Methods and analysis
This study is a randomized clinical trial. Thirty patients with mild to moderate ulcerative colitis will be randomly allocated to receive a low FODMAP diet (n = 15) or to continue their usual diet as control (n = 15), for 4 weeks. The quantity of intestinal microbiota including Clostridium cluster IV, Faecalibacterium prausnitzii, Rosburia spp., Lactobacillus spp., Bifidobacteria spp., Akkermansia muciniphila, Bacteroides fragilis, and Ruminococcus spp., and the Firmicutes to Bacteroidetes ratio and calprotectin and lactoferrin levels will be explored in fecal samples from patients. In addition, anthropometric measures and biochemical assessments including serum concentrations of highly sensitive-C reactive protein (hs-CRP), tumour necrosis factor-α (TNF-α) and IL-1β will be taken from patients at baseline and end of the study. The study has been registered in IRCT (IRCT20181126041763N1; registration date: 2019-01-18).

Discussion
Consumption of a low-FODMAP diet might decrease systemic and intestinal inflammation, change the bacterial population in the gut, and modulate clinical symptoms in patients with ulcerative colitis. Further studies investigating the effect of such a diet on other variables, including other bacterial species and inflammatory cytokines, are required to confirm future findings of this trial.
Update of the ULtra-early TRranexamic Acid after Subarachnoid Hemorrhage (ULTRA) trial: statistical analysis plan
Authors: Post René , Germans Menno R. , Coert Bert A. , Rinkel Gabriël J. E. , Vandertop W. Peter , Verbaan Dagmar 
Published: February 2020

Abstract
Background
Recurrent bleeding from an intracranial aneurysm after subarachnoid hemorrhage (SAH) is associated with unfavorable outcome. Recurrent bleeding before aneurysm occlusion can be performed occurs in up to one in five patients and most often happens within the first 6 h after the primary hemorrhage. Reducing the rate of recurrent bleeding could be a major factor in improving clinical outcome after SAH. Tranexamic acid (TXA) reduces the risk of recurrent bleeding but has thus far not been shown to improve functional outcome, probably because of a higher risk of delayed cerebral ischemia (DCI). To reduce the risk of ultraearly recurrent bleeding, TXA should be administered as soon as possible after diagnosis and before transportation to a tertiary care center. If TXA is administered for a short duration (i.e., < 24 h), it may not increase the risk of DCI. The aim of this paper is to present in detail the statistical analysis plan (SAP) of the ULTRA trial (ULtra-early TRranexamic Acid after Subarachnoid Hemorrhage), which is currently enrolling patients and investigating whether ultraearly and short-term TXA treatment in patients with aneurysmal SAH improves clinical outcome at 6 months.

Methods/design
The ULTRA trial is a multicenter, prospective, randomized, open, blinded endpoint, parallel-group trial currently ongoing at 8 tertiary care centers and 16 of their referral centers in the Netherlands. Participants are randomized to standard care or to receive TXA at a loading dose of 1 g, immediately followed by 1 g every 8 h for a maximum of 24 h, in addition to standard care, as soon as SAH is diagnosed. In the TXA group, TXA administration is stopped immediately prior to treatment (coil or clip) of the causative aneurysm. Primary outcome is the modified Rankin Scale (mRS) score at 6 months after SAH, dichotomized into good (mRS 0–3) and poor (mRS 4–6) outcomes, assessed blind to treatment allocation. Secondary outcomes include case fatalities at 30 days and at 6 months and causes of poor clinical outcome. Safety outcomes are recurrent bleeding, DCI, hydrocephalus, per-procedural complications, and other complications such as infections occurring during hospitalization. Data analyses will be according to this prespecified SAP.

Trial registration
Netherlands Trial Register, NTR3272. Registered on 25 January 2012.
ClinicalTrials.gov, NCT02684812. Registered on 17 February 2016.
A prospective double-blinded randomised control trial comparing robotic arm-assisted functionally aligned total knee arthroplasty versus robotic arm-assisted mechanically aligned total knee arthroplasty
Authors: Kayani Babar , Konan Sujith , Tahmassebi Jenni , Oussedik Sam , Moriarty Peter D. , Haddad Fares S. 
Published: February 2020

AbstractBackgroundTotal knee arthroplasty (TKA) with mechanical alignment (MA) aims to achieve neutral limb alignment in all patients, whereas TKA with functional alignment (FA) aims to restore native, patient-specific anatomy and knee kinematics by manipulating bone resections and fine-tuning implant positioning. The objective of this study is to determine the optimal alignment technique in TKA by comparing patient satisfaction, functional outcomes, implant survivorship, complications, and cost-effectiveness in MA TKA versus FA TKA. Robotic technology will be used to execute the planned implant positioning and limb alignment with high-levels of accuracy in all study patients.Methods and analysisThis prospective double-blinded randomised control trial will include 100 patients with symptomatic knee osteoarthritis undergoing primary robotic arm-assisted TKA. Following informed consent, patients will be randomised to MA TKA (the control group) or FA TKA (the investigation group) at a ratio of 1:1 using an online random number generator. Blinded observers will review patients at regular intervals for 2 years after surgery to record predefined study outcomes relating to postoperative rehabilitation, clinical progress, functional outcomes, accuracy of implant positioning and limb alignment, gait, implant stability, cost-effectiveness, and complications. A superiority study design will be used to evaluate whether FA TKA provides superior outcomes compared to MA TKA. Primary and secondary objectives will be used to quantify and draw inferences on differences in the efficacy of treatment between the two groups. Intention-to-treat and per-protocol population analysis will be undertaken. The following statistical methods will be employed to analyse the data: descriptive statistics, independentttest, pairedttest, analysis of variance, Fisher exact test, chi-square test, and graphical displays. Ethical approval was obtained from the London-Surrey Research Ethics Committee, UK. The study is sponsored by University College London, UK.DiscussionThis is the first study to describe the use of robotic technology to achieve FA TKA, and the only existing clinical trial comparing robotic MA TKA versus robotic FA TKA. The findings of this study will enable an improved understanding of the optimal alignment technique in TKA for achieving high-levels of patient satisfaction, improving functional outcomes, increasing implant survivorship, improving cost-effectiveness, and reducing complications.RegistrationClinicalTrials.gov,NCT04092153. Registered on 17 September 2019.
Identification of proteins from the secretory/excretory products (SEPs) of the branchiuran ectoparasite Argulus foliaceus (Linnaeus, 1758) reveals unique secreted proteins amongst haematophagous ecdysozoa
Authors: AmbuAli Aisha , Monaghan Sean J. , McLean Kevin , Inglis Neil F. , Bekaert Michaël , Wehner Stefanie , Bron James E. 
Published: February 2020

Abstract
Background
It is hypothesised that being a blood-feeding ectoparasite, Argulus foliaceus (Linnaeus, 1758), uses similar mechanisms for digestion and host immune evasion to those used by other haematophagous ecdysozoa, including caligid copepods (e.g. sea louse). We recently described and characterised glands associated with the feeding appendages of A. foliaceus using histological techniques. The work described in the present study is the first undertaken with the objective of identifying and partially characterising the components secreted from these glands using a proteomic approach.

Methods
Argulus foliaceus parasites were sampled from the skin of rainbow trout (Oncorhynchus mykiss), from Loch Fad on the Isle of Bute, Scotland, UK. The proteins from A. foliaceus secretory/excretory products (SEPs) were collected from the supernatant of artificial freshwater conditioned with active adult parasites (n = 5–9 per ml; n = 560 total). Proteins within the SEPs were identified and characterised using LC-ESI-MS/MS analysis. Data are available via ProteomeXchange with identifier PXD016226.

Results
Data mining of a protein database translated from an A. foliaceus dataset using ProteinScape allowed identification of 27 predicted protein sequences from the A. foliaceus SEPs, each protein matching the criteria of 2 peptides with at least 4 contiguous amino acids. Nine proteins had no matching sequence through OmicsBox (Blast2GO) analysis searches suggesting that Argulus spp. may additionally have unique proteins present in their SEPs. SignalP 5.0 software, identified 13 proteins with a signal sequence suggestive of signal peptides and supportive of secreted proteins being identified. Notably, the functional characteristics of identified A. foliaceus proteins/domains have also been described from the salivary glands and saliva of other blood-feeding arthropods such as ticks. Identified proteins included: transporters, peroxidases, metalloproteases, proteases and serine protease inhibitors which are known to play roles in parasite immune evasion/induction (e.g. astacin), immunomodulation (e.g. serpin) and digestion (e.g. trypsin).

Conclusions
To our knowledge, the present study represents the first proteomic analysis undertaken for SEPs from any branchiuran fish louse. Here we reveal possible functional roles of A. foliaceus SEPs in digestion and immunomodulation, with a number of protein families shared with other haematophagous ectoparasites. A number of apparently unique secreted proteins were identified compared to other haematophagous ecdysozoa.
Transcriptional changes in Toxoplasma gondii in response to treatment with monensin
Authors: Zhai Bintao , He Jun-Jun , Elsheikha Hany M. , Li Jie-Xi , Zhu Xing-Quan , Yang Xiaoye 
Published: February 2020

Background
Infection with the apicomplexan protozoan parasite T. gondii can cause severe and potentially fatal cerebral and ocular disease, especially in immunocompromised individuals. The anticoccidial ionophore drug monensin has been shown to have anti-Toxoplasma gondii properties. However, the comprehensive molecular mechanisms that underlie the effect of monensin on T. gondii are still largely unknown. We hypothesized that analysis of T. gondii transcriptional changes induced by monensin treatment can reveal new aspects of the mechanism of action of monensin against T. gondii.

Methods
Porcine kidney (PK)-15 cells were infected with tachyzoites of T. gondii RH strain. Three hours post-infection, PK-15 cells were treated with 0.1 μM monensin, while control cells were treated with medium only. PK-15 cells containing intracellular tachyzoites were harvested at 6 and 24 h post-treatment, and the transcriptomic profiles of T. gondii-infected PK-15 cells were examined using high-throughput RNA sequencing (RNA-seq). Quantitative real-time PCR was used to verify the expression of 15 differentially expressed genes (DEGs) identified by RNA-seq analysis.

Results
A total of 4868 downregulated genes and three upregulated genes were identified in monensin-treated T. gondii, indicating that most of T. gondii genes were suppressed by monensin. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of T. gondii DEGs showed that T. gondii metabolic and cellular pathways were significantly downregulated. Spliceosome, ribosome, and protein processing in endoplasmic reticulum were the top three most significantly enriched pathways out of the 30 highly enriched pathways detected in T. gondii. This result suggests that monensin, via down-regulation of protein biosynthesis in T. gondii, can limit the parasite growth and proliferation.

Conclusions
Our findings provide a comprehensive insight into T. gondii genes and pathways with altered expression following monensin treatment. These data can be further explored to achieve better understanding of the specific mechanism of action of monensin against T. gondii.
The paradox of cancer genes in non-malignant conditions: implications for precision medicine
Authors: Adashek Jacob J. , Kato Shumei , Lippman Scott M. , Kurzrock Razelle 
Published: February 2020

AbstractNext-generation sequencing has enabled patient selection for targeted drugs, some of which have shown remarkable efficacy in cancers that have the cognate molecular signatures. Intriguingly, rapidly emerging data indicate that altered genes representing oncogenic drivers can also be found in sporadic non-malignant conditions, some of which have negligible and/or low potential for transformation to cancer. For instance, activatingKRASmutations are discerned in endometriosis and in brain arteriovenous malformations, inactivatingTP53tumor suppressor mutations in rheumatoid arthritis synovium, andAKT,MAPK, andAMPKpathway gene alterations in the brains of Alzheimer’s disease patients. Furthermore, these types of alterations may also characterize hereditary conditions that result in diverse disabilities and that are associated with a range of lifetime susceptibility to the development of cancer, varying from near universal to no elevated risk. Very recently, the repurposing of targeted cancer drugs for non-malignant conditions that are associated with these genomic alterations has yielded therapeutic successes. For instance, the phenotypic manifestations of CLOVES syndrome, which is characterized by tissue overgrowth and complex vascular anomalies that result from the activation ofPIK3CAmutations, can be ameliorated by the PIK3CA inhibitor alpelisib, which was developed and approved for breast cancer. In this review, we discuss the profound implications of finding molecular alterations in non-malignant conditions that are indistinguishable from those driving cancers, with respect to our understanding of the genomic basis of medicine, the potential confounding effects in early cancer detection that relies on sensitive blood tests for oncogenic mutations, and the possibility of reverse repurposing drugs that are used in oncology in order to ameliorate non-malignant illnesses and/or to prevent the emergence of cancer.