bluuebunny/crossref_metadata_2025_split huggingface dataset:
Asia's First Rigless Subsea Stimulation Using Patented Well Access Technology and a Fully Integrated Service Model
Authors: Avery Mike , Large Robert , Azhar Herman , Wong Kai San , Yusoff Mohd Faizal 
Published: August 2019

Abstract
Asia's first rigless subsea stimulation was executed in 2018, with intervention performed upon three target wells offshore Sabah Malaysia, at a water depth of approximately 1400 m (4,593 ft). Significant changes in reservoir performance prompted an acid stimulation and scale squeeze treatment, designed to remedy fines migration and scaling issues within the well and production system. Treatment fluids were delivered subsea by an open-water hydraulic access system, using a hybrid coiled-tubing downline. Access to the subsea trees was permitted via a patented choke access technology, allowing for a flexible, opex-efficient, and low-risk intervention. The intervention system was installed upon a multi-service vessel, with the downline deployed via the vessel moonpool. A second support vessel was used as required to provide additional fluid capacity without disturbing primary intervention operations. This enhanced the flexibility of the operation, permitting changes in the treatment plan to be accommodated for without impact to critical path stimulation activities.
The full intervention was delivered as an integrated service, with all elements supplied by a single provider, via one contract. An established network of in-house equipment, expertise, test laboratories, and operational bases supported the planning and execution of the project. This was complemented by select external providers for vessels, remotely operated vehicle services, and other specialist contractors.
The challenges faced during this new market entry included completion of a comprehensive treatment fluid test program, importation and logistics of equipment from around the globe, and managing operational risks, all within a condensed timeline to satisfy a brief intervention window. By leveraging the diverse global network of the service provider, the technology and people required for the project were accessed and brought together to achieve a collaborative solution. This was enhanced by the inclusion of performance based elements within the contract. The provision of a highly efficient and flexible well access technology also supported rapid mobilization and operational risk reduction.
Post-stimulation well testing confirmed an average increase in oil productivity of 86%, with a corresponding productivity index factor (PIF) gain of 3.4. These results, combined with the efficient execution of the campaign, confirm the appropriateness of open-water hydraulic access using coiled-tubing for performing cost-effective stimulations on complex subsea wells.
Successful entry to the region was highly dependent upon the integrated nature of the service. Access to the service providers global network permitted a high degree of influence upon the ultimate performance of the stimulation. Examples include the PIF results achieved and the responsive actions taken to remedy offshore challenges such as reservoir lock-up on well #3.
Full-length poly(A) and mRNA sequencing (FLAM-seq)
Authors: Legnini Ivano , Alles Jonathan , Karaiskos Nikos , Ayoub Salah , Quedenau Claudia , Rajewsky Nikolaus 
Published: August 2019

Abstract
We developed FLAM-seq, a fast and simple method for generating cDNA libraries of full-length mRNAs, including the poly(A) tail. By combining a new strategy for cDNA preparation with PacBio long-read sequencing, FLAM-seq enables to generate hundreds of thousands of reads per sample in an easy and short procedure, with starting material ranging from 500 ng to 10 μg of total RNA. Besides the quantification of gene expression and the information about the mRNA isoform, the data generated with FLAM-seq allow accurate measurement of poly(A) tail length for thousands of genes in the sequenced samples. Here we describe the protocol step by step from the RNA preparation to the first steps of data analysis.
Genome-wide identification and expression analysis of PUB genes in cotton
Authors: Lu Xuke , Shu Na , Wang Delong , Wang Junjuan , Chen Xiugui , Zhang Binglei , Wang Shuai , Guo Lixue , Ye Wuwei 
Published: August 2019

Abstract
Background: U-box gene is gene of ubiquitin ligase, which contain U-box domain. Plant U-box gene (PUB) plays an important role in the response to stresses, but less reports about PUBs in cotton were issued. Therefore research of PUBs in cotton will be of great importance and necessity to study the mechanism of tolerance-resistance of the cotton.
Results: In this study, we identified 93, 96, 185 and 208 PUBs from the three sequenced cotton species G. raimondii (D5), G. arboreum (A2), G. hirsutum (AD1) and G. arbadense (AD2), respectively. Subcellular localization analysis showed that the PUBs in cotton were distributed in various parts of the cells, mainly in the nucleus. The PUBs in cotton were divided into six subfamilies (A-F) by phylogenetic analysis, and intron/exon structure was comparatively conserved within the subfamily. Location analysis showed cotton PUBs were unevenly anchored on all the chromosomes varying from 1 to 14. It was found that there are 3 tandem duplications and 28 segmental duplications in cotton genome D5, 2 tandem duplications and 25 segmental duplications in A2, and 143 homologous gene pairs between A2 and D5, through multiple sequence alignment, but that the tandem duplication region of A2 or D5 was not found. It was also found that, there were 105, 14 and 17 homologous gene pairs in intra-subgenome of At and Dt, At subgenome, Dt subgenome of allotetraploid cotton, respectively. Among the PUBs family, totally 106, 116, 85 and 81 homologous gene pairs were found in A2-At, A2-Dt, D5-At and D5-Dt. Function analysis of GhPUB85A and GhPUB45D showed they positively responded the abiotic stresses, but the expression patterns were different. Besides, although the expressions of these two homologous genes were similar, their contributions were different when responding to stresses, showing different response differences to abiotic stresses and function division of two subgenomes of G. hirsutum.
Conclusion: This study provided the genome-wide identification, structure, evolution and expression analysis of PUBs in cotton, and the results showed that the PUBs was highly conserved in evolutionary history of cotton. All PUB genes were involved in response to abiotic stresses at varying degrees.
Does Case-based blended-learning expedite the transfer of declarative knowledge to procedural knowledge in practice?
Authors: Turk Bela Rui , Ertl Sebastian , Wong Guoruey , Wadowski Patricia P , Loeffler-Stastka Henriette 
Published: August 2019

Abstract
Background

Case-Based Learning (CBL) has seen widespread implementation in undergraduate education since the early 1920s. Ample data has shown CBL to be an enjoyable and motivational didactic tool, and effective in assisting the expansion of declarative and procedural knowledge in academia. Although a plethora of studies apply multiple choice questions (MCQs) in their investigation, few studies measure CBL or case-based blended learning (CBBL)-mediated changes in students’ procedural knowledge in practice or employ comparison or control groups in isolating causal relationships.

Methods

Utilizing the flexibilities of an e-learning platform, a CBBL framework consisting of a) anonymized patient cases, b) case-related textbook material and online e-CBL modules, and c) simulated patient (SP) contact seminars, was developed and implemented in multiple medical fields for undergraduate medical education. Additionally, other fields saw a solo implementation of e-CBL in the same format. E- cases were constructed according to the criteria of Bloom’s taxonomy.

In this study, Objective Structured Clinical Examination (OSCE) results from (n=619) medical students in 2013 before CBBL implementation, and after CBBL implementation in 2015 (n=624) and 2016 (n=643) were analyzed.

Results

A significant improvement (adjusted p=.002) of the mean OSCE score by 1.02 points was seen between 2013 and 2015 (min=0, max=25).

Conclusion

E-Case-Based Learning is an effective tool in increasing student satisfaction, improving performance outcomes and may provide a sustainable learning platform for many fields of medicine in future.
Evaluation of Anterior Decompression Surgical Outcomes of Proximal-type Cervical Spondylotic Amyotrophy, a Retrospective Study
Authors: Lu Chang-bo , Ma Zhen-sheng , Hu Jin-bo , Wu Zi-xiang , Yang Xiao-jiang , Wei Wei , Zhang Yang , Lei Wei 
Published: August 2019

Abstract
Background

To investigate the effect of anterior decompression on cervical spondylotic amyotrophy patients with cervical radiculopathy.

Methods

From January 2012 to December 2016, 21 patients with proximal-type cervical spondylotic amyotrophy(CSA) underwent anterior decompression were included. There were 15 males and 6 females, aged 35-73 years with an average of 51.62 years. All underwent surgery of anterior decompression (ACDF or ACCF). Among them, 12 patients underwent C4/5 single level ACDF, 8 patients underwent C4/5 and C5/6 double level ACDF, and one patient underwent C5 anterior cervical corpectomy decompression and fusion surgery. Preoperative and postoperative clinical and radiologic results were assessed. The evaluation items include muscle strength, visual analog scale (VAS) score, neck disability index (NDI) score, Japanese Orthopedic Association (JOA) score, and improvement rate at the last follow-up. Neurological and radiological follow-up averaged 13.2 months.

Results

Severe preoperative muscle atrophy was observed in the deltoid or biceps muscles of 21 patients before surgeries. At the final follow-up, all patients showed statistically improvements in muscle strength, VAS scores, and NDI scores (P<0.05, P<0.05, P<0.05), especially for the deltoid muscles force and JOA scores (P<0.01, P<0.01), of which the average improvement rates were 66.49±10.04% and 62.23±9.23%, respectively.

Conclusions

For CSA patients, especially resulted from cervical radiculopathy, anterior decompression surgery can improve patient's muscle strength and nerve root compression symptoms and generally achieve satisfactory curative effects
The phylogenetic significance of the morphology of the syrinx, hyoid and larynx, of the Southern Cassowary, Casuarius casuarius (Aves, Palaeognathae)
Authors: McInerney Phoebe Louise , Lee Mike S. Y. , Clement Alice M. , Worthy Trevor H. 
Published: August 2019

Abstract
The Palaeognathae are a basal clade within Aves and include the large and flightless ratites and the smaller, volant tinamous. Although much research has been conducted on various aspects of palaeognath morphology, ecology, and evolutionary history, there are still areas which require investigation. This study aimed to fill gaps in our knowledge of the Southern cassowary, Casuarius casuarius, for which information on the syrinx, hyoid and larynx is lacking despite these structures having been recognised as performing key functional roles associated with vocalisation, respiration and feeding. Previous research into the syrinx and hyoid have also indicated these structures to be valuable for determining evolutionary relationships among neognath taxa, and thus may also shed light on palaeognath phylogeny, which still exhibits strong conflict between morphological and molecular trees. We thus documented variation across palaeognaths in syringeal, hyoidal, and laryngeal character states, using both the literature and novel new observations (e.g. of cassowary). Notably the molecular moa-tinamou clade was found to share derived morphological traits including the ossification of the cricoid and arytenoid cartilages, and an additional cranial character, the articulation between the maxillary process of the nasal and the maxilla. Syringeal, hyoidal and laryngeal characters better optimised onto the topology resulting from phylogenetic analyses of a combined molecular and morphology analysis, than molecular-only or morphological-only trees. One primary factor for this support was the aforementioned shared character states between the moa and tinamou, also present in Lithornis and outgroup taxa.
Diverse Effects of Different Akkermansia muciniphila Genotypes on Brown Adipose Tissue Inflammation and Whitening in a High-fat-diet Murine Model
Authors: Deng Lulu , Ou Zihao , Huang Dongquan , Li Chong , Lu Zhi , Liu Wanting , Wu Feifan , Nong Caihong , Gao Jie , Peng Yongzheng 
Published: August 2019

Abstract
Background

The study aimed to investigate the differences of different Akkermansia muciniphila (A.muciniphila) genotypes on metabolic protective effects in mice with high-fat diet and explore possible mechanisms.

Methods

Male C57BL/6 mice were randomly divided into 6 groups, including high-fat diet (HFD)+ A.muciniphila I/II/PBS group, normal chow diet (NCD)+A.muciniphila I/ II /PBS group, respectively. Dietary intervention and A.muciniphila gavage were performed simultaneously. Blood glucose and lipid metabolism, brown adipose morphology and activities, and intestinal barrier function were examined after the mice were sacrificed.

Results

A.muciniphila gavage improved the impaired glucose tolerance, hyperlipidemia and liver steatosis in HFD mice, and that A.muciniphila II was not as effective as A.muciniphila I. This phenomenon might be because A.muciniphila I intervention significantly inhibited brown adipose tissue whitening and inflammation induced by HFD, by repairing the intestinal barrier and relieving endotoxemia. A.muciniphila II did not display the same results as A.muciniphila I in HFD mice, but had stronger effects in the NCD mice.

Conclusions

This study mainly reveals the distinct functions of different A.muciniphila genotypes on diet-induced obesity, suggesting that different A.muciniphila genotypes may play inequitable roles in pathological conditions through distinct action pathways.
Effect and Safety of Anti-PD-1/PD-L1 Monotherapy for Metastatic Breast Cancer: A meta-analysis
Authors: Qi Yihang , Kong Xiangyi , Wang Xiangyu , Zhai Jie , Fang Yi , Wang Jing 
Published: August 2019

Abstract
Background. Given that no approved targeted agents for metastatic triple-negative breast cancer (mTNBC) and no opportunity of surgery for metastatic breast cancer (MBC), new treatment options are urgently to be discovered. The anti-PD-1/PD-L1 immunotherapy may be effective, and what we should be aware of is the response rate and adverse events.
Methods. The PUBMED, EMBASE, Cochrane and www.clinicaltrials.gov databases were searched to find potential studies using the following strategies: anti-PD-1/PD-L1; metastatic; breast cancer. R© package Meta was used to pool incidence.
Results. Six studies including 586 advanced breast cancer patients treated with anti-PD-1/PD-L1 agents were included in this meta-analysis. The anti-PD-1/PD-L1 agents include pembrolizumab, atezolizumab and avelumab. Among these patients, CR was 1.26%, PR was 7.65%, ORR was 9.85% and DCR was 18.33%. We also found that the response rate was closely associated with the expression of PD-L1 biomarker (PD-L1+ vs PD-L1-): the CR was 2.71% vs 0.00%; the PR was 9.93% vs 2.69%; the ORR was 10.62% vs 3.07%; the DCR was 17.95% vs 4.71%. 1-year overall survival rate and 6-months progression-free survival rate were 43.34% and 17.24%. Respectively, the overall incidence of AEs was 64.18% in any grade and 12.94% in severe grade. The incidence of irAEs was 14.75%. Besides, the incidence of discontinue and death due to treatment-related AEs was about 3.06% and 0.31% respectively. When the detailed AEs were analyzed, most treatment-related AEs of any grade were arthraigia, asthenia, decreased appetite; most common treatment-related AEs of severe grade were anemia, autoimmune hepatitis, diarrhea; the most common irAEs were hypothyroidism , followed by hyperthyroidism, pneumonitis and infusion-related reaction.
Conclusions. Anti-PD-1/PD-L1 monotherapy showed a manageable safety profile and had a durable anti-tumor clinical activity in a subset of patients with mTNBC or MBC. PD-L1 expression may be correlated to a higher probability of clinical response.
Silencing of the DJ-1 (PARK7) gene sensitizes pancreatic cancer to erlotinib inhibition
Authors: He Xiangyi , Sun Yunwei , Fan Rong , Sun jing , Zou Douwu , Yuan Yaozong 
Published: August 2019

Abstract
Abstract
AIMS:
The epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor erlotinib, in combination with gemcitabine, has been shown to be a promising therapy in the treatment of pancreatic cancer. Our previous study showed that DJ-1 promotes invasion and metastasis of pancreatic cancer cells by activating SRC/ERK/uPA. The aim of this study was to evaluate whether silencing DJ-1 expression can sensitize pancreatic cancer cells to erlotinib treatment.
METHODS:
Knockdown of DJ-1 expression, combined with erlotinib treatment, was performed in the pancreatic cancer cell lines BxPC-3 and PANC-1. Cell proliferation was assessed with the CCK-8 assay and BrdU incorporation, while apoptosis was measured using terminal deoxynucleotidyl ransferase (TdT)-mediated dUTP nick-end labeling. RAS activity and activation of the downstream pathways involving AKT and ERK1/2 were explored to determine the underlying mechanism.
RESULTS:
Knockdown of DJ-1 expression accelerated erlotinib-induced cell apoptosis, and improved the inhibitory effect of erlotinib on pancreatic cancer cell proliferation in vitro and in xenograft tumor growth in vivo. Knockdown of DJ-1 decreased K-RAS expression, membrane translocation, and activity in BxPC-3 cells. Knockdown of DJ-1 also decreased K-RAS, H-RAS, and N-RAS expression in PANC-1 cells. Knockdown of DJ-1 synergistically inhibited AKT and ERK1/2 phosphorylation with erlotinib in pancreatic cancer cells.
CONCLUSIONS:
DJ-1 may activate the RAS pathway, reinforcing erlotinib drug resistance. Blocking DJ-1 in combination with the EGFR tyrosine kinase inhibitor erlotinib may be an attractive therapeutic target in pancreatic cancer.
FunFam protein families improve residue level molecular function prediction
Authors: Scheibenreif Linus Mathias , Littmann Maria , Orengo Christine , Rost Burkhard 
Published: August 2019

Abstract
Background

The CATH database provides a hierarchical classification of protein domain structures including a sub-classification of superfamilies into functional families (FunFams). We analyzed the similarity of binding site annotations in these FunFams and incorporated FunFams into the prediction of protein binding residues.

Results

FunFam members agreed, on average, in 36.9±0.6% of their binding residue annotations. This constituted a 6.7-fold increase over randomly grouped proteins and a 1.2-fold increase (1.1-fold on the same dataset) over proteins with the same enzymatic function (identical Enzyme Commission, EC, number). Mapping de novo binding site prediction methods (BindPredict-CCS, BindPredict-CC) onto FunFam resulted in consensus predictions for those residues that were aligned and predicted alike (binding/non-binding) within a FunFam. This simple consensus increased the F1-score (for binding) 1.5-fold over the original prediction method. Variation of the threshold for how many proteins in the consensus prediction had to agree provided a convenient control of accuracy/precision and coverage/recall, e.g. reaching a precision as high as 60.8±0.4% for a stringent threshold.

Conclusions

The FunFams outperformed even the carefully curated EC numbers in terms of agreement of binding site residues. Additionally, we assume that our proof-of-principle through the prediction of protein binding residues will be relevant for many other solutions profiting from FunFams to infer functional information at the residue level.
Increased Production of Recombinant O-Phospho-L-Serine Sulfhydrylase from the Hyperthermophilic Archaeon Aeropyrum pernix K1 Using Escherichia coli
Authors: Nakamura Takashi , Takeda Emi , Kiryu Tomoko , Mori Kentaro , Ohori Miyu , Kikugawa Eiki , Ishikawa Kazuhiko 
Published: August 2019

Background:
O-phospho-L-serine sulfhydrylase from the hyperthermophilic archaeon Aeropyrum
pernix K1 (ApOPSS) is thermostable and tolerant to organic solvents. It can produce nonnatural
amino acids in addition to L-cysteine.

Objective:
We aimed to obtain higher amounts of ApOPSS compared to those reported with previous
methods for the convenience of research and for industrial production of L-cysteine and non-natural
amino acids.

Method:
We performed codon optimization of cysO that encodes ApOPSS, for optimal expression in
Escherichia coli. We then examined combinations of conditions such as the host strain, plasmid, culture
medium, and isopropyl β-D-1-thiogalactopyranoside (IPTG) concentration to improve ApOPSS yield.

Results and Discussion:
E. coli strain Rosetta (DE3) harboring the expression plasmid pQE-80L with
the codon-optimized cysO was cultured in Terrific broth with 0.01 mM IPTG at 37°C for 48 h to yield
a 10-times higher amount of purified ApOPSS (650 mg·L-1) compared to that obtained by the conventional
method (64 mg·L-1). We found that the optimal culture conditions along with codon optimization
were essential for the increased ApOPSS production. The expressed ApOPSS had a 6-histidine tag at
the N-terminal, which did not affect its activity. This method may facilitate the industrial production of
cysteine and non-natural amino acids using ApOPSS.

Conclusion:
We conclude that these results could be used in applied research on enzymatic production
of L-cysteine in E. coli, large scale production of non-natural amino acids, an enzymatic reaction in organic
solvent, and environmental remediation by sulfur removal.
Elementary Economic Systems in Material Agent Societies
Authors: Rocha Costa Antônio Carlos 
Published: August 2019

This paper formally characterizes the elementary economic systems of material agent societies, on the bases of the notions of (individual and group) elementary economic behavior, elementary economic exchange and elementary economic process. The equilibrium of an elementary economic system is defined in terms of the equilibrium of the set of group elementary economic processes that constitute such system. A case study illustrates the proposed concepts.
Information Dissemination through Embedded Financial Analysts: Evidence from China
Authors: Li Zengquan , Wong T. J. , Yu Gwen 
Published: August 2019

ABSTRACT
When emerging market firms disclose relationship-based transactions, they face a trade-off in which greater transparency may help lower their cost of capital at the cost of revealing proprietary information. We find that firms overcome this challenge by relying on analysts within their private networks (i.e., connected analysts) who, through repeated interaction with the firm, can better verify relationship-based transactions. Using Chinese firms, we show that firms with more connected analysts have more accurate consensus forecasts and lower forecast dispersion. When a connected analyst departs and stops covering a firm, the accuracy and informativeness of the unconnected analysts' forecasts decrease, suggesting that information spills over from the connected analyst to analysts outside the network. We find a potential mechanism for this information spillover: communication through common institutional clients, which suggests that embedded financial analysts—those sharing close connections with firms and analysts—serve as a channel for disseminating proprietary, hard-to-verify information.
JEL Classifications: G14; G15; M40; N25.
Data Availability: Data are available from sources identified in the text.