bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ultrasound-Guided Proximal and Distal Tarsal Decompression: An Analysis of Pressures in the Tarsal, Medial Plantar, and Lateral Plantar Tunnels
Authors: Iborra Marcos Alvaro , Villanueva Martinez Manuel , Sanz-Ruiz Pablo , Barrett Stephen L. , Zislis George 
Published: February 2020

Objectives. To analyze the reliability of measurements of tarsal tunnel and medial and lateral plantar tunnel pressures before and after ultrasound-guided release. Measurements taken were guided by ultrasound to improve reliability. This novel approach may help surgeons make surgical decisions. The second objective was to confirm that decompression using ultrasound-guided surgery as previously described by the authors is technically effective, reducing pressure to the tarsal and medial and lateral plantar tunnels. Methods. The study included 23 patients with symptoms compatible with idiopathic tarsal tunnel syndrome (TTS). The first step was to measure intracompartmental pressure of the tarsal tunnel, medial plantar tunnel, and lateral plantar tunnel preoperatively. The second step was ultrasound-guided decompression of the tibial nerve and its branches. Subsequently, pressure was measured again immediately after decompression in the 3 tunnels. Results. After surgery, the mean values significantly dropped to normal values. This represents a validation of effective decompression of the tibial nerve and its branches in TTS with ultra–minimally invasive surgery. Conclusions. The ultrasound-guided surgical technique to release the tibial nerve and its branches is effective, significantly reducing pressure in the tunnels and, thereby, decompressing the nerves. Level of evidence: Level IV
Longitudinal Assessment of Quadriceps Muscle Morphology Before and After Anterior Cruciate Ligament Reconstruction and Its Associations With Patient-Reported Outcomes
Authors: Garcia Steven A. , Curran Michael T. , Palmieri-Smith Riann M. 
Published: February 2020

Background: Reductions in muscle size are common after anterior cruciate ligament reconstruction (ACLR) and may contribute to suboptimal patient outcomes. However, few studies have quantified postoperative alterations in muscle quality and evaluated its associations with patient-reported function. Hypotheses: Rectus femoris cross-sectional area (CSA) will decrease postoperatively but improve at return to activity (RTA), rectus femoris muscle quality (percentage fat [PF]) will increase postoperatively and be greater at RTA compared with preoperative values, and rectus femoris CSA and PF will be associated with International Knee Documentation Committee (IKDC) scores at both postoperative time points. Study Design: Case series. Level of Evidence: Level 4. Methods: A total of 26 individuals who sustained an ACL injury and underwent reconstructive surgery were evaluated preoperatively (T0), 9 weeks post-ACLR (T1), and at RTA. Rectus femoris CSA and PF were evaluated bilaterally via ultrasound imaging, and patient-reported function was assessed using the IKDC score. Results: Bilateral reductions in rectus femoris CSA were noted from T0 to T1 ( P < 0.01). Only the uninvolved limb returned to preoperative CSA ( P = 0.80), as the involved limb failed to return to preoperative levels at RTA ( P = 0.04). No significant changes in rectus femoris PF were observed across time points ( P > 0.05). Lesser PF ( P < 0.01) but not CSA ( P = 0.75) was associated with higher IKDC score at T1. Lesser PF ( P = 0.04) and greater CSA ( P = 0.05) was associated with higher IKDC score at RTA. Conclusion: Substantial atrophy occurs bilaterally after ACLR, and the involved limb does not return to preoperative muscle size despite the patient completing rehabilitation. Quadriceps muscle morphology is associated with patient-reported function and may be an important rehabilitation target after ACLR. Clinical Relevance: Quadriceps atrophy and poor muscle quality may contribute to suboptimal patient functioning and quadriceps dysfunction and may be important in RTA decision making. Assessing muscle morphology using ultrasound may be a feasible and clinically beneficial tool in patients after ACLR.
HLA-DRB1 allele impact on pediatric multiple sclerosis in a Hellenic cohort
Authors: Gontika Maria , Skarlis Charalampos , Artemiadis Artemios , Pons Roser , Mastroyianni Sotiria , Vartzelis George , Theodorou Virginia , Kilindireas Konstantinos , Stefanis Leonidas , Dalakas Marinos , Chrousos George , Anagnostouli Maria 
Published: February 2020

Background Pediatric-onset multiple sclerosis (POMS) is considered a complex disease entity with many genetic and environmental factors implicated in its pathogenesis. Linkage studies in Caucasian adult populations consistently demonstrate the major histocompatibility complex and its HLA (human leukocyte antigen) polymorphisms as the genetic locus most strongly linked to MS. Objective To investigate the frequencies and possible clinical and imaging correlations of HLA-DRB1 alleles in a Hellenic POMS sample. Methods Fifty POMS patients fulfilling the IPMSSG (International Pediatric Multiple Sclerosis Study Group) criteria were enrolled using 144 adult-onset MS (AOMS) patients and 246 healthy controls for comparisons. HLA genotyping was performed with standard low-resolution sequence-specific oligonucleotide (SSO) techniques. Clinical and imaging correlations with specific HLA-DRB1 alleles were also examined. Results The HLA-DRB1*03 genotype was significantly higher in POMS patients compared to both the AOMS population (26% vs. 12.5%, p = 0.042) and the general population (26% vs. 12.6%, p = 0.004). HLA-DRB1*03-positive POMS patients had significantly more relapses (6.9 ± 4.9 vs. 4.2 ± 4.4, p = 0.005) and more thoracic spinal cord lesions than HLA-DRB1*03-negative patients (61.5% vs. 27%, p = 0.043). Conclusion In our Hellenic population, HLA-DRB1*03 allele confers increased risk for POMS and it is also correlated with possibly increased disease activity, expanding the existing knowledge on HLA associations and POMS.
C-reactive protein is not a screening tool for late periprosthetic joint infection
Authors: Fink Bernd , Schlumberger Michael , Beyersdorff Julian , Schuster Philipp 
Published: February 2020

Abstract
Background
Preoperative diagnosis of periprosthetic joint infection (PJI) is important because of the therapeutic consequences. The aim of the present study is to investigate whether the serum C-reactive protein (CRP) level can be used as a screening tool for late PJI.

Materials and methods
A cohort of 390 patients with revision surgery of total hip prostheses (200) or total knee prostheses (190) was assessed for late PJI by determining CRP serum level and performing preoperative aspiration with cultivation and intraoperative tissue analyses with cultivation and histologic examination, using the Musculoskeletal Infection Society (MSIS) and International Consensus Meeting (ICM) criteria.

Results
A total of 180 joints were rated as PJI (prevalence 46%). Of these, 42.8% (77) showed a CRP level below 10 mg/L and 28.3% (51) showed a normal CRP level of less than 5 mg/L. The 76.9% of the cases with slow-growing bacteria showed a CRP level below 10 mg/L, and 61.5% showed a normal CRP level.

Conclusions
Serum CRP level should not be used as a screening tool to rule out late PJI.

Level of evidence
Level 2 (diagnostic study).
MOMO - multi-objective metabolic mixed integer optimization: application to yeast strain engineering
Authors: Andrade Ricardo , Doostmohammadi Mahdi , Santos João L. , Sagot Marie-France , Mira Nuno P. , Vinga Susana 
Published: February 2020

Abstract
Background
In this paper, we explore the concept of multi-objective optimization in the field of metabolic engineering when both continuous and integer decision variables are involved in the model. In particular, we propose a multi-objective model that may be used to suggest reaction deletions that maximize and/or minimize several functions simultaneously. The applications may include, among others, the concurrent maximization of a bioproduct and of biomass, or maximization of a bioproduct while minimizing the formation of a given by-product, two common requirements in microbial metabolic engineering.

Results
Production of ethanol by the widely used cell factory Saccharomyces cerevisiae was adopted as a case study to demonstrate the usefulness of the proposed approach in identifying genetic manipulations that improve productivity and yield of this economically highly relevant bioproduct. We did an in vivo validation and we could show that some of the predicted deletions exhibit increased ethanol levels in comparison with the wild-type strain.

Conclusions
The multi-objective programming framework we developed, called Momo, is open-source and uses PolySCIP (Available at http://polyscip.zib.de/). as underlying multi-objective solver. Momo is available at http://momo-sysbio.gforge.inria.fr
Equivalent change enrichment analysis: assessing equivalent and inverse change in biological pathways between diverse experiments
Authors: Thompson Jeffrey A. , Koestler Devin C. 
Published: February 2020

Abstract
Background
In silico functional genomics have become a driving force in the way we interpret and use gene expression data, enabling researchers to understand which biological pathways are likely to be affected by the treatments or conditions being studied. There are many approaches to functional genomics, but a number of popular methods determine if a set of modified genes has a higher than expected overlap with genes known to function as part of a pathway (functional enrichment testing). Recently, researchers have started to apply such analyses in a new way: to ask if the data they are collecting show similar disruptions to biological functions compared to reference data. Examples include studying whether similar pathways are perturbed in smokers vs. users of e-cigarettes, or whether a new mouse model of schizophrenia is justified, based on its similarity in cytokine expression to a previously published model. However, there is a dearth of robust statistical methods for testing hypotheses related to these questions and most researchers resort to ad hoc approaches. The goal of this work is to develop a statistical approach to identifying gene pathways that are equivalently (or inversely) changed across two experimental conditions.

Results
We developed Equivalent Change Enrichment Analysis (ECEA). This is a new type of gene enrichment analysis based on a statistic that we call the equivalent change index (ECI). An ECI of 1 represents a gene that was over or under-expressed (compared to control) to the same degree across two experiments. Using this statistic, we present an approach to identifying pathways that are changed in similar or opposing ways across experiments. We compare our approach to current methods on simulated data and show that ECEA is able to recover pathways exhibiting such changes even when they exhibit complex patterns of regulation, which other approaches are unable to do. On biological data, our approach recovered pathways that appear directly connected to the condition being studied.

Conclusions
ECEA provides a new way to perform gene enrichment analysis that allows researchers to compare their data to existing datasets and determine if a treatment will cause similar or opposing genomic perturbations.
Dynamic network inference and association computation discover gene modules regulating virulence, mycotoxin and sexual reproduction in Fusarium graminearum
Authors: Guo Li , Ji Mengjie , Ye Kai 
Published: February 2020

Abstract
Background
The filamentous fungus Fusarium graminearum causes devastating crop diseases and produces harmful mycotoxins worldwide. Understanding the complex F. graminearum transcriptional regulatory networks (TRNs) is vital for effective disease management. Reconstructing F. graminearum dynamic TRNs, an NP (non-deterministic polynomial) -hard problem, remains unsolved using commonly adopted reductionist or co-expression based approaches. Multi-omic data such as fungal genomic, transcriptomic data and phenomic data are vital to but so far have been largely isolated and untapped for unraveling phenotype-specific TRNs.

Results
Here for the first time, we harnessed these resources to infer global TRNs for F. graminearum using a Bayesian network based algorithm called “Module Networks”. The inferred TRNs contain 49 regulatory modules that show condition-specific gene regulation. Through a thorough validation based on prior biological knowledge including functional annotations and TF binding site enrichment, our network prediction displayed high accuracy and concordance with existing knowledge. One regulatory module was partially validated using network perturbations caused by Tri6 and Tri10 gene disruptions, as well as using Tri6 Chip-seq data. We then developed a novel computational method to calculate the associations between modules and phenotypes, and identified major module groups regulating different phenotypes. As a result, we identified TRN subnetworks responsible for F. graminearum virulence, sexual reproduction and mycotoxin production, pinpointing phenotype-associated modules and key regulators. Finally, we found a clear compartmentalization of TRN modules in core and lineage-specific genomic regions in F. graminearum, reflecting the evolution of the TRNs in fungal speciation.

Conclusions
This system-level reconstruction of filamentous fungal TRNs provides novel insights into the intricate networks of gene regulation that underlie key processes in F. graminearum pathobiology and offers promise for the development of improved disease control strategies.
Detrimental Effects of Filling Laryngotracheal Airways To Excessive Pressure (DEFLATE-P): a quality improvement initiative
Authors: Fritz Ashley V. , Mickus Gregory J. , Vega Michael A. , Renew J. Ross , Brull Sorin J. 
Published: February 2020

Abstract
Background
This quality improvement (QI) project was performed at a single center to determine the incidence of postoperative complications associated with use of cuffed airway devices. An educational program was then completed that involved training our anesthesia providers about complications related to excessive cuff pressure and how to utilize a quantitative cuff pressure measurement device (manometer). The impact of this educational initiative was assessed by comparing the incidence of postoperative complications associated with the use of airway devices before and after the training period.

Methods
After approval by our institution’s Institutional Review Board, a pre-intervention (baseline) survey was obtained from 259 adult patients after having undergone surgery with general anesthesia with the use of an endotracheal tube (ETT) or laryngeal mask airway (LMA). Survey responses were used to determine the baseline incidence of sore throat, hoarseness, and dysphagia. Once these results were obtained, education was provided to the anesthesia department members addressing the complications associated with excessive cuff pressures, appropriate cuff pressures based on manufacturer recommendations, and instructions on the use of a quantitative monitor to determine cuff pressure (manometry). Clinical care was then changed by requiring intraoperative cuff pressure monitoring throughout our institution for all surgical patients. After this educational period, 299 patients completed the same survey describing postoperative airway complications.

Results
The use of manometry reduced the incidence of moderate-to-severe postoperative sore throat in the pre- vs. post-intervention groups (35 patients vs 31 patients, p = 0.045), moderate to severe hoarseness (30 patients vs 13, patients p = 0.0001), and moderate-to-severe dysphagia (13 patients vs 5 patients, p = 0.03).

Conclusion
Caring for patients in the perioperative setting frequently entails placement of an airway device. This procedure is associated with several potential complications, including sore throat, coughing, and vocal cord damage. Our quality improvement initiative has shown that intraoperative management of intra-cuff pressure based on manometry is feasible to implement in clinical practice and can reduce postoperative airway complications.
Consecutive electrocardiographic changes during percutaneous coronary intervention for acute coronary syndrome with high-grade atrioventricular block: a case report
Authors: Sueyoshi Hiroyuki , Akita Yuzo , Oishi Yohei , Mukai Yu , Hagino Tomoko , Yutaka Kotaro , Matsui Yumie , Yoshinaga Masahiro , Karakawa Masahiro , Mori Yasukiyo 
Published: February 2020

Abstract
Background
Acute coronary syndrome (ACS) with high-grade atrioventricular block (HAVB) still has a poor mortality risk, even in the current percutaneous coronary intervention (PCI) era. However, early PCI for ACS with HAVB is associated with improved in-hospital survival and a 6-month survival similar to that of ACS without HAVB.

Case presentation
A 70-year-old man was admitted to our hospital for ACS with HAVB. ECG showed complete AV block, complete right bundle branch block (CRBBB), and left axis deviation. Cardiac enzymes were elevated. He underwent temporary pacemaker insertion and coronary angiography, which showed severe stenosis of the proximal right coronary artery (RCA), 99% stenosis of the distal RCA with Thrombolysis in Myocardial Infarction (TIMI) grade 2 flow, and total occlusion of the proximal left anterior descending artery (LAD). We performed primary PCI in both the RCA and LAD, which resulted in TIMI grade 3 flow in both. After PCI, the HAVB recovered to normal sinus rhythm with CRBBB; a normal QRS interval returned within three days. The patient was discharged from the hospital without complications.

Conclusion
In this case of ACS with HAVB, early intensive coronary artery reperfusion resulted in long-term patient survival. The blood supply to the AV node and bilateral bundle branches is complex. Multivessel ischemia may compromise both primary and collateral blood flows to the AV node and septum, resulting in severe conduction impairment. Clinicians performing PCI should be aware of this anatomy and physiology.
Isolated central nervous system Aspergillosis infection in a chronic lymphocytic leukemia patient on Ibrutinib: A case report
Authors: Le Thuy-Hong , Kumar Vikas , Gondal Khubaib , Barnes Martin , Siddique Haseeb , Buttar Barjinder , Kaell Alan 
Published: February 2020

Abstract
Background
In patients at high risk of opportunistic infections who present with isolated.
neurological symptoms, it is lifesaving to consider Central Nervous System Aspergillosis (CNS-A). Ibrutinib use in chronic lymphocytic leukemia (CLL) has previously been associated with CNS-A. We provide a case report of a patient that presented with primary CNS-A on Ibrutinib therapy without any prior pulmonary or local paranasal signs of infection.

Case presentation
74-year-old Caucasian male with CLL and no prior chemotherapy on ibrutinib for 6 months presented with three months of unsteady gait, occipital headache, and confusion. He has a history of pulmonary sarcoidosis on chronic prednisone 5 mg daily and chronic obstructive pulmonary disease (COPD). He was found to have a “brain abscess” on imaging. Emergent craniotomy confirmed Aspergillus and patient was treated with Voriconazole for 6 months. At six-month follow up, repeat magnetic resonance imaging (MRI) confirmed complete resolution of CNS lesion.

Conclusions
Our case reinforces the importance of being vigilant for isolated CNS-A in CLL patients on ibrutinib who present with neurological symptoms and signs, without prior or co-infection of sino-pulmonary tissue.
Association between maternal sleep duration and quality, and the risk of preterm birth: a systematic review and meta-analysis of observational studies
Authors: Wang Ling , Jin Feng 
Published: February 2020

AbstractBackgroundTo assess the association of sleep duration and quality with the risk of preterm birth.MethodsRelevant studies were retrieved from the PubMed and Web of Science databases up to September 30, 2018. The reference lists of the retrieved articles were reviewed. Random effects models were applied to estimate summarized relative risks (RRs) and 95% confidence intervals (CIs).ResultsTen identified studies (nine cohort studies and one case-controlled study) examined the associations of sleep duration and quality with the risk of preterm birth. As compared with women with the longest sleep duration, the summary RR was 1.23 (95% CI = 1.01–1.50) for women with the shortest sleep duration, with moderate between-study heterogeneity (I2 = 57.4%). Additionally, as compared with women with good sleep quality, the summary RR was 1.54 (95% CI = 1.18–2.01) for women with poor sleep quality (Pittsburgh Sleep Quality Index > 5), with high between-study heterogeneity (I2 = 76.7%). Funnel plots as well as the Egger’s and Begg’s tests revealed no evidence of publication bias.ConclusionsThis systematic review and meta-analysis revealed that short sleep duration and poor sleep quality may be associated with an increased risk of preterm birth. Further subgroup analyses are warranted to test the robustness of these findings as well as to identify potential sources of heterogeneity.
A treat and extend protocol with Aflibercept for cystoid macular oedema secondary to central retinal vein occlusion – an 18-month prospective cohort study
Authors: O’Day Roderick , Ali Noha , Lim Lyndell L. , Sandhu Sukhpal , Chau Thuy , Wickremasinghe Sanjeewa 
Published: February 2020

Abstract
Background
To evaluate the safety and efficacy of a treat-and-extend protocol of aflibercept for cystoid macular oedema (CMO) secondary to central retinal vein occlusion (CRVO).

Methods
Twenty patients with CMO secondary to CRVO were included in this prospective cohort study. After 3 loading 4-weekly injections, treatment intervals were increased by 2 weeks if there was no clinical activity, to a maximum of 12 weeks. If clinical activity recurred or persisted, the interval between injections was shortened by 2 weeks, to a minimum of 4 weeks. Main outcome measures were change in visual acuity and the proportion of patients gaining 15 or more Early Treatment of Diabetic Retinopathy Study (ETDRS) letters from baseline at 6, 12 and 18 months.

Results
Mean BCVA gain from baseline was 19.7 ± 13.8, 22.2 ± 13.9 and 21.9 ± 15.8 ETDRS letters at 6, 12 and 18 months, respectively. Sixty-five percent of patients gained 15 or more ETDRS letters at 6 months, increasing to 70.6% at 12 and 18 months. Patients received 5.0 [4.0 to 6.0], 8.5 [8.0 to 10.3] and 11.0 [9.0 to 12.5] injections by 6, 12 and 18 months, respectively.

Conclusions
The visual outcomes achieved with a treat-and-extend protocol in this study were similar to the pivotal trials of aflibercept for CMO secondary to CRVO, which used monthly and then as-needed protocols.

Trial registration
Australian and New Zealand Clinical Trials Registry, registration number ACTRN12615000417583, 01/05/2015.