bluuebunny/crossref_metadata_2025_split huggingface dataset:
Distinct transcriptome profiles reveal gene expression patterns during fruit development and maturation in five main cultivated species of pear (Pyrus L.)
Authors: Zhang Ming-Yue , Xue Cheng , Xu Linlin , Sun Honghe , Qin Meng-Fan , Zhang Shaoling , Wu Jun 
Published: June 2016

AbstractThe transcriptomes of five pear cultivars, ‘Hosui’ (P. pyrifolia), ‘Yali’ (P. bretschneideri), ‘Kuerlexiangli’ (P. sinkiangensis), ‘Nanguoli’ (P. ussuriensis) and ‘Starkrimson’ (P. communis) were sequenced at seven key fruit developmental stages, from fruit setting to maturation and fruit senescence after harvesting. In total, 33,136 genes that could be mapped by reads, were analyzed. Most gene expression cluster models showed a steadily decreasing trend. Gene expression patterns had obvious differences according to maturity type, that is, post-ripening cultivars were still vigorous at maturity and showed a higher proportion of up-regulated genes; non post-ripening cultivars had a gradually decreasing tendency during fruit maturation. Meanwhile, differentially expressed genes related to fruit quality and development, such as stone cells, sugar, acid and hormones, were identified. Co-expression analysis revealed that several ethylene synthesis genes and polyphenoloxidase-related genes interacted with each other directly and an indirect relationship was reflected between ethylene synthesis genes and ethylene response genes. In addition, the highly diverse SNPs represented the great differences between oriental and occidental pears. Understanding how RNA-seq based gene-expression patterns and differential gene expression contribute to fruit quality allows us to build models for gene-expression for fruit development of Pyrus species.
Combination therapy with polymyxin B and netropsin against clinical isolates of multidrug-resistant Acinetobacter baumannii
Authors: Chung Joon-hui , Bhat Abhayprasad , Kim Chang-Jin , Yong Dongeun , Ryu Choong-Min 
Published: June 2016

AbstractPolymyxins are last-resort antibiotics for treating infections of Gram-negative bacteria. The recent emergence of polymyxin-resistant bacteria, however, urgently demands clinical optimisation of polymyxin use to minimise further evolution of resistance. In this study we developed a novel combination therapy using minimal concentrations of polymyxin B. After large-scale screening of Streptomyces secondary metabolites, we identified a reliable polymixin synergist and confirmed as netropsin using high-pressure liquid chromatography, nuclear magnetic resonance and mass spectrometry followed by in vitro assays using various Gram-negative pathogenic bacteria. To evaluate the effectiveness of combining polymixin B and netropsin in vivo, we performed survival analysis on greater wax moth Galleria mellonella infected with colistin-resistant clinical Acinetobacter baumannii isolates as well as Escherichia coli, Shigella flexineri, Salmonella typhimuruim, and Pseudomonas aeruginosa. The survival of infected G. mellonella was significantly higher when treated with polymyxin B and netropsin in combination than when treated with polymyxin B or netropsin alone. We propose a netropsin combination therapy that minimises the use of polymyxin B when treating infections with multidrug resistant Gram-negative bacteria.
Naïve CD8+ T cell derived tumor-specific cytotoxic effectors as a potential remedy for overcoming TGF-β immunosuppression in the tumor microenvironment
Authors: Nguyen Hong Hanh , Kim Therasa , Song Sang Yun , Park Somang , Cho Hyang Hee , Jung Sung-Hoon , Ahn Jae-Sook , Kim Hyeoung-Joon , Lee Je-Jung , Kim Hee-Ok , Cho Jae-Ho , Yang Deok-Hwan 
Published: June 2016

AbstractDespite of the potential implications for cancer immunotherapy, conventional approaches using in vitro expanded CD8+ T cells have suboptimal outcomes, mostly due to loss of functionality from cellular exhaustion. We therefore investigated the phenotypic and functional differences among in vitro activated CD8+ T cells of three different sources, namely naïve (NTeff), memory (MTeff) and tumor-infiltrating lymphocytes (TILeff) from human and mice, to better understand mechanisms behind potent effector functions and potential for overcoming current limitations. In line with the greater proliferation activity and longer telomere lengths of NTeff populations, cells of naïve origin exhibited significantly less amounts of T cell exhaustion markers than those of MTeff and TILeff, and moreover, acquired distinct expression patterns of memory-promoting transcription factors, T-bet and Eomes, induced in a rapid and sustainable manner. NTeff cells appeared to have lower expression of Foxp1 and were refractory to apoptosis upon TGF-β conditioning, implying better survival potential and resistance to tumor-induced immune suppression. Of CD8+ T cell pools activated to tumor-specific CTLs, naïve cell generated effectors possessed the most potent cytotoxic activity, validating implications for use in rational design of adoptive immunotherapy.
Electronic Structures of Free-Standing Nanowires made from Indirect Bandgap Semiconductor Gallium Phosphide
Authors: Liao Gaohua , Luo Ning , Chen Ke-Qiu , Xu H. Q. 
Published: June 2016

AbstractWe present a theoretical study of the electronic structures of freestanding nanowires made from gallium phosphide (GaP)—a III-V semiconductor with an indirect bulk bandgap. We consider [001]-oriented GaP nanowires with square and rectangular cross sections and [111]-oriented GaP nanowires with hexagonal cross sections. Based on tight binding models, both the band structures and wave functions of the nanowires are calculated. For the [001]-oriented GaP nanowires, the bands show anti-crossing structures, while the bands of the [111]-oriented nanowires display crossing structures. Two minima are observed in the conduction bands, while the maximum of the valence bands is always at the Γ-point. Using double group theory, we analyze the symmetry properties of the lowest conduction band states and highest valence band states of GaP nanowires with different sizes and directions. The band state wave functions of the lowest conduction bands and the highest valence bands of the nanowires are evaluated by spatial probability distributions. For practical use, we fit the confinement energies of the electrons and holes in the nanowires to obtain an empirical formula.
Reward disrupts reactivated human skill memory
Authors: Dayan Eran , Laor-Maayany Rony , Censor Nitzan 
Published: June 2016

AbstractAccumulating evidence across species and memory domains shows that when an existing memory is reactivated, it becomes susceptible to modifications. However, the potential role of reward signals in these mechanisms underlying human memory dynamics is unknown. Leaning on a wealth of findings on the role of reward in reinforcing memory, we tested the impact of reinforcing a skill memory trace with monetary reward following memory reactivation, on strengthening of the memory trace. Reinforcing reactivated memories did not strengthen the memory, but rather led to disruption of the memory trace, breaking down the link between memory reactivation and subsequent memory strength. Statistical modeling further revealed a strong mediating role for memory reactivation in linking between memory encoding and subsequent memory strength only when the memory was replayed without reinforcement. We suggest that, rather than reinforcing the existing memory trace, reward creates a competing memory trace, impairing expression of the original reward-free memory. This mechanism sheds light on the processes underlying skill acquisition, having wide translational implications.
APMP.T-K3.4: key comparison of realizations of the ITS-90 over the range -38.8344 °C to 419.527 °C
Authors: Joung W , Gam K S , Achmadi A , Trisna B A 
Published: June 2016

The APMP bilateral key comparison APMP.T-K3.4 was initiated on the request from RCM-LIPI (Indonesia) to link their national standards to the average reference values (ARVs) of the CCT-K3. Korea Research Institute of Standards and Science (KRISS, Republic of Korea) provided the linkage to the CCT-K3 for temperatures ranging from -38.8344 °C to 419.527 °C. In the APMP.T-K3.4, two standard platinum resistance thermometers (SPRTs) were chosen as the transfer instruments and were calibrated at the ITS-90 fixed-points in the comparison range. The fixed-points in this comparison included Zn freezing point (419.527 °C), Sn freezing point (231.928 °C), In freezing point (156.5985 °C), Ga melting point (29.7646 °C), and Hg triple point (-38.8344 °C). The comparison was carried out in a participant-pilot-participant sequence where KRISS served as the pilot. The linkage was based on the fixed-point resistance ratios of RCM-LIPI relative to the ARVs of the CCT-K3 via the difference between the fixed-point resistance ratios of KRISS and the ARVs of the CCT-K3. The temperature differences between the national standards of RCM-LIPI and the ARVs of the CCT-K3 were within the evaluated comparison uncertainties of the ATPM.T-K3.4. This report provides detailed information on the comparison results, linkage mechanism, and the Degree of Equivalence of the RCM-LIPI relative to the institutes having participated in the CCT-K3.

Main text

To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/.
The final report has been peer-reviewed and approved for publication by the CCT, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
Pharmacokinetics of Tacrolimus and Cyclosporine in Liver Transplant Recipients Receiving 3 Direct-Acting Antivirals as Treatment for Hepatitis C Infection
Authors: Badri Prajakta S. , Parikh Apurvasena , Coakley Eoin P. , Ding Bifeng , Awni Walid M. , Dutta Sandeep , Menon Rajeev M. 
Published: June 2016

Background:
Interactions between tacrolimus and cyclosporine (CSA) and the 3 direct-acting antiviral regimen (3D) of ombitasvir, paritaprevir/ritonavir, and dasabuvir necessitate a priori dose adjustments for the immunosuppressants to achieve desired levels. Modeling and simulations based on data in healthy subjects predicted that tacrolimus 0.5 mg every 7 days or 0.2 mg every 3 days, and CSA at one-fifth the total daily dose administered once daily, would achieve desired trough concentrations (C
trough) during 3D treatment. The success of these dosing recommendations was evaluated by analyzing pharmacokinetic data from liver transplant recipients in the CORAL-I study.

Methods:
A population pharmacokinetic model was developed using tacrolimus dosing and C
trough data before and during 3D treatment (n = 29). The model was used to simulate various tacrolimus dosing regimens and predict tacrolimus concentration–time profiles during 3D treatment. CSA C
trough data before and during 3D treatment (n = 5) were also summarized.

Results:
A one-compartment model with first-order absorption adequately described tacrolimus pharmacokinetic profiles during the first 4 weeks of 3D treatment. Estimated tacrolimus C
trough values (median; interquartile range) before and during 3D treatment were comparable (5.7 ng/mL; 4.9–6.5 ng/mL versus 5.2 ng/mL; 4.2–6.3 ng/mL, respectively). Based on simulations, in a patient with a starting C
trough of 6 ng/mL, 0.5 mg tacrolimus every 7 or 14 days or 0.2 mg tacrolimus every 3 days will result in C
trough levels of 6–9 ng/mL, 4–6 ng/mL, and 6–10 ng/mL, respectively, during 3D treatment. For CSA, C
trough values (median; interquartile range) before and during 3D treatment were comparable (126 ng/mL; 94–140 ng/mL versus 104 ng/mL; 82–140 ng/mL).

Conclusions:
Observed data for tacrolimus and CSA in liver transplant recipients confirm that the recommended dosing strategies are valid and therapeutic levels of immunosuppression can be maintained during 3D treatment.
MACULA RETINAL VASCULITIS AND CHOROIDITIS ASSOCIATED WITH GRANULOMATOSIS WITH POLYANGIITIS
Authors: Lim Lik Thai , Vasudevan Vinaya , Shelton Julie , Vitale Albert T. , Moorthy Ramana 
Published: June 2016

Purpose:
To report a case series of two cases of granulomatosis with polyangiitis, previously known as Wegener granulomatosis, which developed macular necrosis, not previously associated with granulomatosis with polyangiitis, healed with fibrosis, despite aggressive immune-modulating therapy and good control of systemic disease.

Methods:
Case series of two cases with observation of treatment progress.

Results:
The results reported the progress of response to treatment in the two cases, which resulted in the final outcome of fibrosis in the macula region, despite being on aggressive immune-modulating therapy and good systemic control.

Conclusion:
Granulomatosis with polyangiitis can be associated with macular necrosis leading to fibrosis, unresponsive to immune-modulating therapy.
OCULAR MANIFESTATIONS OF MONOCLONAL IMMUNOGLOBULIN LIGHT CHAIN DEPOSITION DISEASE
Authors: Dhrami-Gavazi Elona , Freund K. Bailey , Lee Winston , Cohen Ben Z. , Seshan Surya V. , Yannuzzi Lawrence A. 
Published: June 2016

Purpose:
To demonstrate unusual retinal findings in a patient with progressive renal failure due to idiopathic monoclonal immunoglobulin light chain deposition disease, using multimodal imaging.

Methods:
Observational case report of a 43-year-old white man with renal failure due to light chain deposition disease. His course over 6 years was documented with multimodal imaging including fundus photography, fundus autofluorescence, fluorescein angiography, and spectral domain optical coherence tomography. Additional evaluations included ocular ultrasound, electroretinography, positron emission tomography, serum protein electrophoreses, skeletal surveys to detect osteolytic lesions, and renal, liver, and rectal biopsies in search of amyloid.

Results:
The patient's ocular course mirrored the severity of his renal dysfunction for which he required a renal transplant. Changes observed in the native kidney recurred in the transplant 2 years later, as evidenced by immunohistochemistry, revealing thick linear deposits of kappa chains, with no complement, overlying the glomerular basement membrane. The systemic workup was negative for amyloid but showed an overwhelming ratio of kappa to lambda light chains on serum protein electrophoreses and no clinical signs of plasma cell dyscrasias, all consistent with idiopathic light chain deposition disease. The patient presented with a generalized, bilateral “leopard-spot” fundus appearance on fundus autofluorescence, striking globular subretinal deposits on spectral domain optical coherence tomography, and subfoveal subretinal fluid without retinal pigment epithelium detachment or choroidal effusions. The subfoveal fluid did not respond to intravitreal injections of antiangiogenic agents or steroids but resolved after renal transplantation. A temporary posttransplant visual improvement was associated with lessening of the subretinal drusenoid deposits demonstrated by multimodal imaging. The terminal vision deterioration was associated with amorphous, vitelliform-like material deposition and atrophic changes.

Conclusion:
This case may illustrate a resemblance in the renal glomerulus basement membrane and retinal pigment epithelium–Bruch membrane complex, because the authors observed deposits of excess monoclonal kappa chains manifesting as extracellular, proteinaceous aggregates on the basement membrane of the glomerulus, and striking, globular subretinal deposits that overlay a thickened retinal pigment epithelium–Bruch membrane complex. The ocular lesions' refractoriness to intravitreal treatments could be attributed to the fact that they represent proteinaceous aggregates similar to those documented in the glomeruli. This is the first report of generalized, large, subretinal drusenoid deposits and their course, as documented through multimodal imaging, paralleling the chronology of systemic changes in a patient with light chain deposition disease.
Diabetes Mellitus is Associated With Higher Risk of Developing Decompensated Cirrhosis in Chronic Hepatitis C Patients
Authors: Saeed Mohammed J. , Olsen Margaret A. , Powderly William G. , Presti Rachel M. 
Published: June 2016

Goals:
To investigate the association of diabetes with risk of decompensated cirrhosis in patients with chronic hepatitis C (CHC).

Background:
Direct-acting antivirals are highly effective in treating CHC but very expensive. CHC patients at high risk of progression to symptomatic liver disease may benefit most from early treatment.

Study:
We conducted a retrospective cohort study using the 2006 to 2013 Truven Health Analytics MarketScan Commercial Claims and Encounters database including inpatient, outpatient, and pharmacy claims from private insurers. CHC and cirrhosis were identified using ICD-9-CM diagnosis codes; baseline diabetes was identified by diagnosis codes or antidiabetic medications. CHC patients were followed to identify decompensated cirrhosis. Multivariable Cox proportional hazards regression was used to model the risk of decompensated cirrhosis by baseline cirrhosis.

Results:
There were 75,805 CHC patients with median 1.9 years follow-up. A total of 10,317 (13.6%) of the CHC population had diabetes. The rates of decompensated cirrhosis per 1000 person-years were: 185.5 for persons with baseline cirrhosis and diabetes, 119.8 for persons with cirrhosis and no diabetes, 35.3 for persons with no cirrhosis and diabetes, and 17.1 for persons with no cirrhosis and no diabetes. Diabetes was associated with increased risk of decompensated cirrhosis in persons with baseline cirrhosis (adjusted hazard ratio=1.4; 95% confidence interval, 1.3-1.6) and in persons without baseline cirrhosis (adjusted hazard ratio=1.9; 95% confidence interval, 1.7-2.1).

Conclusions:
In a privately insured US population with CHC, the adjusted risk of decompensated cirrhosis was higher in diabetic compared with nondiabetic patients. Diabetes status should be included in prioritization of antiviral treatment.
Complete Platysma Transection in Neck Rejuvenation: A Critical Appraisal
Authors: Pelle-Ceravolo Mario , Angelini Matteo , Silvi Erminia 
Published: June 2016

Background:
The most common features of aging in the anterior neck are skin laxity and anterior platysma bands. Most neck correction techniques fail to obtain lasting correction of these despite promising early improvement. The authors use a major procedure to obtain the best results, combining full neck undermining with complete platysma transection and midline platysma approximation. Even using this technique, the authors have had concerns about the long-term results, and are aware of the lack of published studies of results using this technique.

Methods:
A prospective study was conducted on 150 consecutive neck-lift patients operated on by the same senior surgeon (M.P.C.) between 2010 and 2014 to evaluate patient satisfaction and recurrence rates of anterior skin laxity and platysma bands. Patients were reviewed at 3 months (138 cases) and 1 year (96 cases). At both time points, patients completed questionnaires on level of satisfaction and eventual complaints regarding their surgical treatment, and were objectively evaluated for skin excess and recurrent bands.

Results:
At 1 year, 76 percent of the patients were satisfied with the outcome using this technique, although satisfaction had been 100 percent at 3 months. However, only 52 percent showed no anterior neck skin excess and 55 percent had no recurrence of bands 1 year after surgery.

Conclusions:
Despite obtaining satisfactory results in most patients, this technique has several downsides: it is time consuming, there is the risk of iatrogenic deformities unless it is carried out precisely, the postoperative recovery is often very long, and there is a significant failure to maintain long-term correction. After 25 years’ experience with these deficiencies, a reconsideration of the most appropriate procedure for correction of the anterior neck is warranted.

CLINICAL QUESTION/LEVEL OF EVIDENCE:
Therapeutic, IV.
Outbreaks associated with duodenoscopes: new challenges and controversies
Authors: Rubin Zachary A. , Murthy Rekha K. 
Published: June 2016

Purpose of review
Recent outbreaks of carbapenem-resistant enterobacteriaceae related to duodenoscopes in the United States and Europe have gained international attention and resulted in new regulations, especially in the United States, affecting healthcare facilities. In this review, we summarize findings from recent duodenoscope-related outbreaks, highlight what is known about the risk of transmission from these devices and discuss controversies about current recommendations to prevent transmission.

Recent findings
Between 2013 and 2015, several US and European healthcare facilities reported outbreaks of carbapenem-resistant enterobacteriaceae associated with endoscopic retrograde cholangiopancreatography procedures. Unlike prior outbreaks (attributed to lapses in cleaning and reprocessing), the recent outbreaks occurred in spite of adherence to current reprocessing guidelines. Factors associated with infection transmission include a low margin of safety for gastrointestinal endoscopic procedures and complex design features of duodenoscopes. Outbreaks were halted with enhanced cleaning and surveillance measures or by adopting gas sterilization methods. New guidance from manufacturers and federal agencies has been issued as a result of these recent outbreaks; however, concerns remain that the new measures may not eliminate risks to patients.

Summary
Recent duodenoscope-related outbreaks have highlighted the need for a reassessment of current guidelines for endoscope reprocessing and for new design of duodenoscope components. Although we summarize the US experience, this review has global implications for the safe cleaning and disinfection of these instruments.