bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cartilage Restoration of Patellofemoral Lesions: A Systematic Review
Authors: Andrade Renato , Nunes Joni , Hinckel Betina B. , Gruskay Jordan , Vasta Sebastiano , Bastos Ricardo , Oliveira J. Miguel , Reis Rui L. , Gomoll Andreas H. , Espregueira-Mendes João 
Published: December 2019

Purpose This study aimed to systematically analyze the postoperative clinical, functional, and imaging outcomes, complications, reoperations, and failures following patellofemoral cartilage restoration surgery. Methods This review was conducted according to the guidelines of Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA). PubMed, EMBASE, and Cochrane Library databases were searched up to August 31, 2018, to identify clinical studies that assessed surgical outcomes of patellofemoral cartilage restoration surgery. The Methodological Index for Non-Randomized Studies (MINORS) was used to assess study quality. Results Forty-two studies were included comprising 1,311 knees (mean age of 33.7 years and 56% males) and 1,309 patellofemoral defects (891 patella, 254 trochlear, 95 bipolar, and 69 multiple defects, including the patella or trochlea) at a mean follow-up of 59.2 months. Restoration techniques included autologous chondrocyte implantation (56%), particulated juvenile allograft cartilage (12%), autologous matrix-induced chondrogenesis (9%), osteochondral autologous transplantation (9%), and osteochondral allograft transplantation (7%). Significant improvement in at least one score was present in almost all studies and these surpassed the minimal clinically important difference threshold. There was a weighted 19%, 35%, and 6% rate of reported complications, reoperations, and failures, respectively. Concomitant patellofemoral surgery (51% of patients) mostly did not lead to statistically different postoperative outcomes. Conclusion Numerous patellofemoral restoration techniques result in significant functional improvement with a low rate of failure. No definitive conclusions could be made to determine the best surgical technique since comparative studies on this topic are rare, and treatment choice should be made according to specific patient and defect characteristics. Level of evidence Level IV, systematic review of level II to IV studies.
Read-SpaM: assembly-free and alignment-free comparison of bacterial genomes with low sequencing coverage
Authors: Lau Anna-Katharina , Dörrer Svenja , Leimeister Chris-André , Bleidorn Christoph , Morgenstern Burkhard 
Published: December 2019

AbstractBackgroundIn many fields of biomedical research, it is important to estimate phylogenetic distances between taxa based on low-coverage sequencing reads. Major applications are, for example, phylogeny reconstruction, species identification from small sequencing samples, or bacterial strain typing in medical diagnostics.ResultsWe adapted our previously developed software programFiltered Spaced-Word Matches (FSWM)for alignment-free phylogeny reconstruction to take unassembled reads as input; we call this implementationRead-SpaM.ConclusionsTest runs on simulated reads from semi-artificial and real-world bacterial genomes show that our approach can estimate phylogenetic distances with high accuracy, even for large evolutionary distances and for very low sequencing coverage.
Recovering rearranged cancer chromosomes from karyotype graphs
Authors: Aganezov Sergey , Zban Ilya , Aksenov Vitaly , Alexeev Nikita , Schatz Michael C. 
Published: December 2019

Abstract
Background
Many cancer genomes are extensively rearranged with highly aberrant chromosomal karyotypes. Structural and copy number variations in cancer genomes can be determined via abnormal mapping of sequenced reads to the reference genome. Recently it became possible to reconcile both of these types of large-scale variations into a karyotype graph representation of the rearranged cancer genomes. Such a representation, however, does not directly describe the linear and/or circular structure of the underlying rearranged cancer chromosomes, thus limiting possible analysis of cancer genomes somatic evolutionary process as well as functional genomic changes brought by the large-scale genome rearrangements.

Results
Here we address the aforementioned limitation by introducing a novel methodological framework for recovering rearranged cancer chromosomes from karyotype graphs. For a cancer karyotype graph we formulate an Eulerian Decomposition Problem (EDP) of finding a collection of linear and/or circular rearranged cancer chromosomes that are determined by the graph. We derive and prove computational complexities for several variations of the EDP. We then demonstrate that Eulerian decomposition of the cancer karyotype graphs is not always unique and present the Consistent Contig Covering Problem (CCCP) of recovering unambiguous cancer contigs from the cancer karyotype graph, and describe a novel algorithm capable of solving CCCP in polynomial time. We apply on a prostate cancer dataset and demonstrate that it is capable of consistently recovering large cancer contigs even when underlying cancer genomes are highly rearranged.

Conclusions
can recover rearranged cancer contigs from karyotype graphs thereby addressing existing limitation in inferring chromosomal structures of rearranged cancer genomes and advancing our understanding of both patient/cancer-specific as well as the overall genetic instability in cancer.
A retrospective study of the relationship between postoperative urine output and one year transplanted kidney function
Authors: Kim Joungmin , Pyeon Taehee , Choi Jeong Il , Kang Jeong Hyeon , Song Seung Won , Bae Hong-Beom , Jeong Seongtae 
Published: December 2019

Abstract
Background
Kidney transplantation (KT) is the most obvious method of treating a patient with end-stage renal disease. In the early stages of KT, urine production is considered a marker of successful reperfusion of the kidney after anastomosis. However, there is no clear conclusion about the relationship between initial urine output after KT and 1-year renal function. Thus, we investigated the factors that affect 1-year kidney function after KT, including urine output.

Methods
This retrospective study investigated the relationship between urine output in the 3 days after KT and transplanted kidney prognosis after 1-year. In total, 291 patients (129 living-donor and 162 deceased-donor transplant recipients) were analyzed; 24-h urine volume per body weight (in kilograms) was measured for 3 days postoperatively. The estimated glomerular filtration rate (eGFR), determined by the Modification of Diet in Renal Disease algorithm, was used as an index of renal function. Patients were grouped according to eGFR at 1-year after KT: a good residual function group, eGFR ≥60, and a poor residual function group, eGFR < 60.

Result
Recipients’ factors affecting 1-year eGFR include height (P = 0.03), weight (P = 0.00), and body mass index (P = 0.00). Donor factors affecting 1-year eGFR include age (P = 0.00) and number of human leukocyte antigen (HLA) mismatches (P = 0.00). The urine output for 3 days after KT (postoperative day 1; 2 and 3) was associated with 1-year eGFR in deceased-donor (P = 0.00; P = 0.00 and P = 0.01). And, postoperative urine output was associated with the occurrence of delayed graft function (area under curve (AUC) = 0.913; AUC = 0.984 and AUC = 0.944).

Conclusion
Although postoperative urine output alone is not enough to predict 1-year GFR, the incidence of delayed graft function can be predicted. Also, the appropriate urine output after KT may differ depending on the type of the transplanted kidney.

Trial registration
Clinical Research Information Service of the Korea National Institute of Health in the Republic of Korea (KCT0003571).
Comparison of general anesthesia with endotracheal intubation, combined spinal-epidural anesthesia, and general anesthesia with laryngeal mask airway and nerve block for intertrochanteric fracture surgeries in elderly patients: a retrospective cohort study
Authors: Liu Yang , Su Mang , Li Wei , Yuan Hao , Yang Cheng 
Published: December 2019

Abstract
Background
There is no consensus on the optimal anesthesia method for intertrochanteric fracture surgeries in elderly patients. Our study aimed to compare the hemodynamics and perioperative outcomes of general anesthesia with endotracheal intubation, combined spinal-epidural anesthesia, and general anesthesia with laryngeal mask airway (LMA) and nerve block for intertrochanteric fracture surgeries in elderly patients.

Methods
This is a retrospective study of 75 patients aged > 60 years scheduled for intertrochanteric fracture surgeries with general anesthesia with intubation (n = 25), combined spinal-epidural anesthesia (n = 25), and general anesthesia with LMA and nerve block (n = 25). The intraoperative hemodynamics were recorded, and the maximum variation rate was calculated. Postoperative analgesic effect was evaluated using the visual analog scale (VAS). Postoperative cognitive status was assessed using the Mini-Mental State Exam (MMSE).

Results
The maximum variation rate of intraoperative heart rate, systolic blood pressure, diastolic blood pressure differed significantly between the three groups (general anesthesia with intubation > combined spinal-epidural anesthesia > general anesthesia with LMA and nerve block). The VAS scores postoperative 2 h, 4 h, 6 h, and 8 h also differed significantly between the three groups (general anesthesia with intubation > combined spinal-epidural anesthesia > general anesthesia with LMA and nerve block). The VAS scores postoperative 24 h were significantly lower in the general anesthesia with LMA/nerve block group than the general anesthesia with intubation group and the combined spinal-epidural anesthesia group. The MMSE scores postoperative 15 min and 45 min differed significantly between the three groups (general anesthesia with intubation < combined spinal-epidural anesthesia < general anesthesia with LMA and nerve block). The MMSE scores postoperative 120 min in the general anesthesia with intubation group were the lowest among the three groups. There was no significant difference in the incidence of respiratory infection postoperative 24 h, 48 h, and 72 h between the three groups.

Conclusion
Compared to general anesthesia with intubation and combined spinal-epidural anesthesia, general anesthesia with LMA and nerve block had better postoperative analgesic effect and less disturbances on intraoperative hemodynamics and postoperative cognition for elderly patients undergoing intertrochanteric fracture surgeries.
Intrathecal injection of bone marrow stromal cells attenuates neuropathic pain via inhibition of P2X4R in spinal cord microglia
Authors: Teng Yongbo , Zhang Yang , Yue Shouwei , Chen Huanwen , Qu Yujuan , Wei Hui , Jia Xiaofeng 
Published: December 2019

Abstract
Background
Neuropathic pain is one of the most debilitating of all chronic pain syndromes. Intrathecal (i.t.) bone marrow stromal cell (BMSC) injections have a favorable safety profile; however, results have been inconsistent, and complete understanding of how BMSCs affect neuropathic pain remains elusive.

Methods
We evaluated the analgesic effect of BMSCs on neuropathic pain in a chronic compression of the dorsal root ganglion (CCD) model. We analyzed the effect of BMSCs on microglia reactivity and expression of purinergic receptor P2X4 (P2X4R). Furthermore, we assessed the effect of BMSCs on the expression of transient receptor potential vanilloid 4 (TRPV4), a key molecule in the pathogenesis of neuropathic pain, in dorsal root ganglion (DRG) neurons.

Results
I.t. BMSC transiently but significantly ameliorated neuropathic pain behavior (37.6% reduction for 2 days). We found no evidence of BMSC infiltration into the spinal cord parenchyma or DRGs, and we also demonstrated that intrathecal injection of BMSC-lysates provides similar relief. These findings suggest that the analgesic effects of i.t. BMSC were largely due to the release of BMSC-derived factors into the intrathecal space. Mechanistically, we found that while i.t. BMSCs did not change TRPV4 expression in DRG neurons, there was a significant reduction of P2X4R expression in the spinal cord microglia. BMSC-lysate also reduced P2X4R expression in activated microglia in vitro. Coadministration of additional pharmacological interventions targeting P2X4R confirmed that modulation of P2X4R might be a key mechanism for the analgesic effects of i.t. BMSC.

Conclusion
Altogether, our results suggest that i.t. BMSC is an effective and safe treatment of neuropathic pain and provides novel evidence that BMSC’s analgesic effects are largely mediated by the release of BMSC-derived factors resulting in microglial P2X4R downregulation.
Chronic dry eye induced corneal hypersensitivity, neuroinflammatory responses, and synaptic plasticity in the mouse trigeminal brainstem
Authors: Fakih Darine , Zhao Zhanlin , Nicolle Pierre , Reboussin Elodie , Joubert Fanny , Luzu Jade , Labbé Antoine , Rostène William , Baudouin Christophe , Mélik Parsadaniantz Stéphane , Réaux-Le Goazigo Annabelle 
Published: December 2019

AbstractBackgroundDry eye disease (DED) is a multifactorial disease associated with ocular surface inflammation, pain, and nerve abnormalities. We studied the peripheral and central neuroinflammatory responses that occur during persistent DED using molecular, cellular, behavioral, and electrophysiological approaches.MethodsA mouse model of DED was obtained by unilateral excision of the extraorbital lachrymal gland (ELG) and Harderian gland (HG) of adult female C57BL/6 mice. In vivo tests were conducted at 7, 14, and 21 days (d) after surgery. Tear production was measured by a phenol red test and corneal alterations and inflammation were assessed by fluorescein staining and in vivo confocal microscopy. Corneal nerve morphology was evaluated by nerve staining. Mechanical corneal sensitivity was monitored using von Frey filaments. Multi-unit extracellular recording of ciliary nerve fiber activity was used to monitor spontaneous corneal nerve activity. RT-qPCR and immunostaining were used to determine RNA and protein levels at d21.ResultsWe observed a marked reduction of tear production and the development of corneal inflammation at d7, d14, and d21 post-surgery in DED animals. Chronic DE induced a reduction of intraepithelial corneal nerve terminals. Behavioral and electrophysiological studies showed that the DED animals developed time-dependent mechanical corneal hypersensitivity accompanied by increased spontaneous ciliary nerve fiber electrical activity. Consistent with these findings, DED mice exhibited central presynaptic plasticity, demonstrated by a higher Piccolo immunoreactivity in the ipsilateral trigeminal brainstem sensory complex (TBSC). At d21 post-surgery, mRNA levels of pro-inflammatory (IL-6 and IL-1β), astrocyte (GFAP), and oxidative (iNOS2 and NOX4) markers increased significantly in the ipsilateral trigeminal ganglion (TG). This correlated with an increase in Iba1, GFAP, and ATF3 immunostaining in the ipsilateral TG of DED animals. Furthermore, pro-inflammatory cytokines (IL-6, TNFα, IL-1β, and CCL2), iNOS2, neuronal (ATF3 and FOS), and microglial (CD68 and Itgam) markers were also upregulated in the TBSC of DED animals at d21, along with increased immunoreactivity against GFAP and Iba1.ConclusionsOverall, these data highlight peripheral sensitization and neuroinflammatory responses that participate in the development and maintenance of dry eye-related pain. This model may be useful to identify new analgesic molecules to alleviate ocular pain.
A high-throughput quantification of resin and rubber contents in Parthenium argentatum using near-infrared (NIR) spectroscopy
Authors: Luo Zinan , Thorp Kelly R. , Abdel-Haleem Hussein 
Published: December 2019

Abstract
Background
Guayule (Parthenium argentatum A. Gray), a plant native to semi-arid regions of northern Mexico and southern Texas in the United States, is an alternative source for natural rubber (NR). Rapid screening tools are needed to replace the current labor-intensive and cost-inefficient method for quantifying rubber and resin contents. Near-infrared (NIR) spectroscopy is a promising technique that simplifies and speeds up the quantification procedure without losing precision. In this study, two spectral instruments were used to rapidly quantify resin and rubber contents in 315 ground samples harvested from a guayule germplasm collection grown under different irrigation conditions at Maricopa, AZ. The effects of eight different pretreatment approaches on improving prediction models using partial least squares regression (PLSR) were investigated and compared. Important characteristic wavelengths that contribute to prominent absorbance peaks were identified.

Results
Using two different NIR devices, ASD FieldSpec®3 performed better than Polychromix Phazir™ in improving R2 and residual predicative deviation (RPD) values of PLSR models. Compared to the models based on full-range spectra (750–2500 nm), using a subset of wavelengths (1100–2400 nm) with high sensitivity to guayule rubber and resin contents could lead to better prediction accuracy. The prediction power of the models for quantifying resin content was better than rubber content.

Conclusions
In summary, the calibrated PLSR models for resin and rubber contents were successfully developed for a diverse guayule germplasm collection and were applied to roughly screen samples in a low-cost and efficient way. This improved efficiency could enable breeders to rapidly screen large guayule populations to identify cultivars that are high in rubber and resin contents.
Nanotechnology in cancer diagnosis: progress, challenges and opportunities
Authors: Zhang Ye , Li Maoyu , Gao Xiaomei , Chen Yongheng , Liu Ting 
Published: December 2019

AbstractIn the fight against cancer, early detection is a key factor for successful treatment. However, the detection of cancer in the early stage has been hindered by the intrinsic limits of conventional cancer diagnostic methods. Nanotechnology provides high sensitivity, specificity, and multiplexed measurement capacity and has therefore been investigated for the detection of extracellular cancer biomarkers and cancer cells, as well as for in vivo imaging. This review summarizes the latest developments in nanotechnology applications for cancer diagnosis. In addition, the challenges in the translation of nanotechnology-based diagnostic methods into clinical applications are discussed.
Improving hydrocarbon production by engineering cyanobacterial acyl-(acyl carrier protein) reductase
Authors: Kudo Hisashi , Hayashi Yuuki , Arai Munehito 
Published: December 2019

Abstract
Background
Acyl-(acyl carrier protein (ACP)) reductase (AAR) is a key enzyme for hydrocarbon biosynthesis in cyanobacteria, reducing fatty acyl-ACPs to aldehydes, which are then converted into hydrocarbons by aldehyde-deformylating oxygenase (ADO). Previously, we compared AARs from various cyanobacteria and found that hydrocarbon yield in Escherichia coli coexpressing AAR and ADO was highest for AAR from Synechococcus elongatus PCC 7942 (7942AAR), which has high substrate affinity for 18-carbon fatty acyl-ACP, resulting in production of mainly heptadecene. In contrast, the hydrocarbon yield was lowest for AAR from Synechococcus sp. PCC 7336 (7336AAR), which has a high specificity for 16-carbon substrates, leading to production of mainly pentadecane. However, even the most productive AAR (7942AAR) still showed low activity; thus, residues within AAR that are nonconserved, but may still be important in hydrocarbon production need to be identified to engineer enzymes with improved hydrocarbon yields. Moreover, AAR mutants that favor shorter alkane production will be useful for producing diesel fuels with decreased freezing temperatures. Here, we aimed to identify such residues and design a highly productive and specific enzyme for hydrocarbon biosynthesis in E. coli.

Results
We introduced single amino acid substitutions into the least productive AAR (7336AAR) to make its amino acid sequence similar to that of the most productive enzyme (7942AAR). From the analysis of 41 mutants, we identified 6 mutations that increased either the activity or amount of soluble AAR, leading to a hydrocarbon yield improvement in E. coli coexpressing ADO. Moreover, by combining these mutations, we successfully created 7336AAR mutants with ~ 70-fold increased hydrocarbon production, especially for pentadecane, when compared with that of wild-type 7336AAR. Strikingly, the hydrocarbon yield was higher in the multiple mutants of 7336AAR than in 7942AAR.

Conclusions
We successfully designed AAR mutants that, when coexpressed with ADO in E. coli, are more highly effective in hydrocarbon production, especially for pentadecane, than wild-type AARs. Our results provide a series of highly productive AARs with different substrate specificities, enabling the production of a variety of hydrocarbons in E. coli that may be used as biofuels.
Different interpretation of additional evidence for HTA by the commissioned HTA body and the commissioning decision maker in Germany: whenever IQWiG and Federal Joint Committee disagree
Authors: Dintsios C. M. , Worm F. , Ruof J. , Herpers M. 
Published: December 2019

Abstract
Background
The purpose of this study was to analyse the impact of commissioned addenda by the Federal Joint Committee (FJC) to the HTA body (IQWiG) and their agreement with FJC decisions and to identify potential additional decisive factors of FJC.

Methods
All available relevant documents up to end of 2017 were screened and essential content extracted. Next to descriptive statistics, differences between IQWiG and FJC were tested and explored by agreement statistics (Cohen’s kappa and Fleiss’ kappa) and ordinal logistic regression.

Results
Most of the 90 addenda concerned oncological products. In all contingent comparisons, positive changes in added benefit or evidence level on a subpopulation basis (n = 124) prevailed negative ones. Fleiss’ ordinal kappa for agreement of assessments, addenda, and appraisals reached a moderate strength for added benefit (0.474, 95%-CI, 0.408–0.540). Overall agreement between addenda and appraisals on a binary nominal basis is poor for added benefit (Cohen’s kappa 0.183; 95%-CI: 0.010–0.357) ranging from “less than by chance” (respiratory diseases) to “perfect” (neurological diseases). The OR of the selected regression model showed that i) mortality, ii) unmet need, the positions of iii) the physicians’ drug commission and iv) medical societies, and v) the annual therapeutic costs of the appropriate comparative therapy had a high influence on FJC’s appraisals deviating from IQWiG’s addenda recommendation.

Conclusions
IQWiG’s addenda have a high impact on decision-maker’s appraisals offering additional analyses of supplementary evidence submitted by the manufacturers. Nevertheless, the agreement between addenda and appraisals varies, highlighting different decisive factors between IQWiG and FJC.
Existence of solutions for some two-point fractional boundary value problems under barrier strip conditions
Authors: Li Zhiyu , Bai Zhanbing 
Published: December 2019

AbstractIn this paper, we are dedicated to researching the boundary value problems (BVPs) for equation$D^{\alpha }x(t)=f(t,x(t),D^{\alpha -1}x(t))$Dαx(t)=f(t,x(t),Dα−1x(t)), with the boundary value conditions to be either:$x(0)=A$x(0)=A,$D^{\alpha -1}x(1)=B$Dα−1x(1)=Bor$D^{\alpha -1}x(0)=A$Dα−1x(0)=A,$x(1)=B$x(1)=B. Let the nonlinear termfsatisfy some sign conditions, then by making use of the Leray–Schauder nonlinear alternative, some existence results are obtained. In the end, an example is given to verify the main results.