bluuebunny/crossref_metadata_2025_split huggingface dataset:
A programmable CRISPR/Cas9-based phage defense system for Escherichia coli BL21(DE3)
Authors: Liu Li , Zhao Dongdong , Ye Lijun , Zhan Tao , Xiong Bin , Hu Muzi , Bi Changhao , Zhang Xueli 
Published: July 2020

AbstractEscherichia coli BL21 is arguably the most popular host for industrial production of proteins, and industrial fermentations are often plagued by phage infections. The CRISPR/Cas system is guided by a gRNA to cleave a specific DNA cassette, which can be developed into a highly efficient programable phage defense system. In this work, we constructed a CRISPR/Cas system targeting multiple positions on the genome of T7 phage and found that the system increased the BL21’s defense ability against phage infection. Furthermore, the targeted loci on phage genome played a critical role. For better control of expression of CRISPR/Cas9, various modes were tested, and the OD of the optimized strain BL21(pT7cas9, pT7-3gRNA, prfp) after 4 h of phage infection was significantly improved, reaching 2.0, which was similar to the control culture without phage infection. Although at later time points, the defensive ability of CRISPR/Cas9 systems were not as obvious as that at early time points. The viable cell count of the engineered strain in the presence of phage was only one order of magnitude lower than that of the strain with no infection, which further demonstrated the effectiveness of the CRISPR/Cas9 phage defense system. Finally, the engineered BL21 strain under phage attack expressed RFP protein at about 60% of the un-infected control, which was significantly higher than the parent BL21. In this work, we successfully constructed a programable CRISPR/Cas9 system to increase the ability of E. coli BL21’s to defend against phage infection, and created a resistant protein expression host. This work provides a simple and feasible strategy for protecting industrial E. coli strains against phage infection.
Ex vivo innate responses to particulate matter from livestock farms in asthma patients and healthy individuals
Authors: de Groot Linsey E. S. , Liu Dingyu , Dierdorp Barbara S. , Fens Niki , van de Pol Marianne A. , Sterk Peter J. , Kulik Wim , Gerlofs-Nijland Miriam E. , Cassee Flemming R. , Pinelli Elena , Lutter René 
Published: July 2020

Abstract
Background
Asthma patients suffer from periodic acute worsening of symptoms (i.e. loss of asthma control or exacerbations), triggered by a variety of exogenous stimuli. With the growing awareness that air pollutants impact respiratory diseases, we investigated whether particulate matter (PM) derived from various livestock farms (BioPM) differentially affected innate and oxidative stress responses in asthma and health.

Methods
Peripheral blood mononuclear cells (PBMCs), collected from patients sequentially before and during loss of asthma control and from healthy individuals, were exposed to BioPM collected from chicken, goat and pig farms (1 and 5 μg/ml), with or without pre-treatment with antioxidants. Cytokine release and oxidative stress were assessed.

Results
PBMCs produced IFNγ, IL-1β, IL-10 and TNFα upon stimulation with BioPM, with that from pig farms inducing the highest cytokine levels. Overall, cytokine production was irrespective of the presence or state of disease. However, PBMCs from stable asthma patients upon exposure to the three BioPM showed more extreme TNFα responses than those from healthy subjects. Furthermore, PBMCs obtained during loss of asthma control that were exposed to BioPM from pig farms showed enhanced IFNγ release as well as decreased oxidative stress levels upon pre-treatment with N-acetylcysteine (NAC) compared to stable disease. NAC, but not superoxide dismutase and catalase, also counteracted BioPM-induced cytokine release, indicating the importance of intracellular reactive oxygen species in the production of cytokines.

Conclusions
BioPM triggered enhanced pro-inflammatory responses by PBMCs from both healthy subjects and asthma patients, with those from patients during loss of asthma control showing increased susceptibility to BioPM from pig farms in particular.
Presence of a 34-gene signature is a favorable prognostic marker in squamous non-small cell lung carcinoma
Authors: Theelen W. S. M. E. , Krijgsman O. , Monkhorst K. , Kuilman T. , Peters D. D. G. C. , Cornelissen S. , Ligtenberg M. A. , Willems S. M. , Blaauwgeers J. L. G. , van Noesel C. J. M. , Peeper D. S. , van den Heuvel M. M. , Schulze K. 
Published: July 2020

Abstract
Background
The tumor immune microenvironment is a heterogeneous entity. Gene expression analysis allows us to perform comprehensive immunoprofiling and may assist in dissecting the different components of the immune infiltrate. As gene expression analysis also provides information regarding tumor cells, differences in interactions between the immune system and specific tumor characteristics can also be explored. This study aims to gain further insights in the composition of the tumor immune infiltrate and to correlate these components to histology and overall survival in non-small cell lung cancer (NSCLC).

Methods
Archival tissues from 530 early stage, resected NSCLC patients with annotated tumor and patient characteristics were analyzed using the NanoString nCounter Analysis system.

Results
Unsupervised clustering of the samples was mainly driven by the overall level of inflammation, which was not correlated with survival in this patient set. Adenocarcinoma (AD) showed a significantly higher degree of immune infiltration compared to squamous cell carcinoma (SCC). A 34-gene signature, which did not correlate with the overall level of immune infiltration, was identified and showed an OS benefit in SCC. Strikingly, this benefit was not observed in AD. This difference in OS in SCC specifically was confirmed in two independent NSCLC cohorts. The highest correlation between expression of the 34-gene signature and specific immune cell populations was observed for NK cells, but although a plausible mechanism for NK cell intervention in tumor growth could be established in SCC over AD, this could not be translated back to immunohistochemistry, which showed that NK cell infiltration is scarce irrespective of histology.

Conclusions
These findings suggest that the ability of immune cell infiltration and the interaction between tumor and immune cells may be different between AD and SCC histology and that a subgroup of SCC tumors seems more susceptible to Natural Killer cell recognition and killing, whereas this may not occur in AD tumors. A highly sensitive technique like NanoString was able to detect this subgroup based on a 34-gene signature, but further research will be needed to assist in explaining the biological rationale of such low-level expression signatures.
NTCP gene polymorphisms and hepatitis B virus infection status in a Ghanaian population
Authors: Nyarko Eric , Obirikorang Christian , Owiredu W. K. B. A. , Adu Evans Asamoah , Acheampong Emmanuel , Aidoo Freeman , Ofori Emmanuel , Addy Bright Selorm , Asare-Anane Henry 
Published: July 2020

Abstract
Background
SLC10A1 gene codes NTCP, a receptor through which the hepatitis B virus (HBV) gets access into hepatocytes - a stage of the viral cycle necessary for replication. Polymorphism variants of SLC10A1 play roles in HBV infection, viral clearance, treatment outcome, and complications, in diverse ethnic groups and countries. However, no such study has been conducted in the Ghanaian population, a country with HBV endemicity. Therefore, an exploratory study was conducted to investigate the presence of three (3) single nucleotide polymorphisms (SNPs) in the SLC10A1 gene (rs2296651, rs61745930, and rs4646287) and assessed the risk of HBV infection among the Ghanaian population.

Method
Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method was used to determine the presence of the SNPs among 292 participants comprising 146 HBV infected persons as case-subjects and 146 HBV non-infected persons as control-subjects.

Results
The minor allele frequency (T) of rs2296651 was present in a significantly high proportion of cases compared with the control group (11.6% vs. 3.1%, p < 0.0001). The homozygote recessive variant of rs61745930 was present in 2.7% of the control group and 5.5% of the case group. Moreover, the minor allele frequencies of rs4646287 were 9.3 and 8.2% among the control and the case group, respectively (p = 0.767). Under the dominant (CC) genetic model of inheritance, rs2296651 was found to be protective of HBV infection [OR = 0.18 (0.07–0.44)], whereas under the co-dominant and additive model, rs2296651 was a potential risk factor for HBV infection [OR = 5.2 (95%CI: 2.1–12.8); 3.5 (95%CI: 1.6–7.6], respectively. Variants of rs61745930 and rs4646287 were not associated with HBV infection (p > 0.05). Polymorphisms in SLC10A1, however, did not show any significant association with HBV infectivity (p > 0.05).

Conclusion
The study highlights some polymorphism proof that variants rs2296651, rs61745930, and rs4646287 exist in HBV-infected individuals in Ghana. Although variant rs2296651 was found to be associated with HBV infection, this association warrants more studies. Polymorphisms in SLC10A1 were not associated with HBV infectivity among the Ghanaian population. Further investigation is warranted to assess the offensive role of the relationship between rs2296651 and HBV infectivity.
Evaluation of novel precision viticulture tool for canopy biomass estimation and missing plant detection based on 2.5D and 3D approaches using RGB images acquired by UAV platform
Authors: Di Gennaro Salvatore Filippo , Matese Alessandro 
Published: July 2020

Abstract
Background
The knowledge of vine vegetative status within a vineyard plays a key role in canopy management in order to achieve a correct vine balance and reach the final desired yield/quality. Detailed information about canopy architecture and missing plants distribution provides useful support for farmers/winegrowers to optimize canopy management practices and the replanting process, respectively. In the last decade, there has been a progressive diffusion of UAV (Unmanned Aerial Vehicles) technologies for Precision Viticulture purposes, as fast and accurate methodologies for spatial variability of geometric plant parameters. The aim of this study was to implement an unsupervised and integrated procedure of biomass estimation and missing plants detection, using both the 2.5D-surface and 3D-alphashape methods.

Results
Both methods showed good overall accuracy respect to ground truth biomass measurements with high values of R2 (0.71 and 0.80 for 2.5D and 3D, respectively). The 2.5D method led to an overestimation since it is derived by considering the vine as rectangular cuboid form. On the contrary, the 3D method provided more accurate results as a consequence of the alphashape algorithm, which is capable to detect each single shoot and holes within the canopy. Regarding the missing plants detection, the 3D approach confirmed better performance in cases of hidden conditions by shoots of adjacent plants or sparse canopy with some empty spaces along the row, where the 2.5D method based on the length of section of the row with lower thickness than the threshold used (0.10 m), tended to return false negatives and false positives, respectively.

Conclusions
This paper describes a rapid and objective tool for the farmer to promptly identify canopy management strategies and drive replanting decisions. The 3D approach provided results closer to real canopy volume and higher performance in missing plant detection. However, the dense cloud based analysis required more processing time. In a future perspective, given the continuous technological evolution in terms of computing performance, the overcoming of the current limit represented by the pre- and post-processing phases of the large image dataset should mainstream this methodology.
Causes and characteristics of death in patients with acute hypoxemic respiratory failure and acute respiratory distress syndrome: a retrospective cohort study
Authors: Ketcham Scott W. , Sedhai Yub Raj , Miller H. Catherine , Bolig Thomas C. , Ludwig Amy , Co Ivan , Claar Dru , McSparron Jakob I. , Prescott Hallie C. , Sjoding Michael W. 
Published: July 2020

AbstractBackgroundAcute hypoxemic respiratory failure (AHRF) and acute respiratory distress syndrome (ARDS) are associated with high in-hospital mortality. However, in cohorts of ARDS patients from the 1990s, patients more commonly died from sepsis or multi-organ failure rather than refractory hypoxemia. Given increased attention to lung-protective ventilation and sepsis treatment in the past 25 years, we hypothesized that causes of death may be different among contemporary cohorts. These differences may provide clinicians with insight into targets for future therapeutic interventions.MethodsWe identified adult patients hospitalized at a single tertiary care center (2016–2017) with AHRF, defined as PaO2/FiO2≤ 300 while receiving invasive mechanical ventilation for > 12 h, who died during hospitalization. ARDS was adjudicated by multiple physicians using the Berlin definition. Separate abstractors blinded to ARDS status collected data on organ dysfunction and withdrawal of life support using a standardized tool. The primary cause of death was defined as the organ system that most directly contributed to death or withdrawal of life support.ResultsWe identified 385 decedents with AHRF, of whom 127 (33%) had ARDS. The most common primary causes of death were sepsis (26%), pulmonary dysfunction (22%), and neurologic dysfunction (19%). Multi-organ failure was present in 70% at time of death, most commonly due to sepsis (50% of all patients), and 70% were on significant respiratory support at the time of death. Only 2% of patients had insupportable oxygenation or ventilation. Eighty-five percent died following withdrawal of life support. Patients with ARDS more often had pulmonary dysfunction as the primary cause of death (28% vs 19%;p = 0.04) and were also more likely to die while requiring significant respiratory support (82% vs 64%;p <  0.01).ConclusionsIn this contemporary cohort of patients with AHRF, the most common primary causes of death were sepsis and pulmonary dysfunction, but few patients had insupportable oxygenation or ventilation. The vast majority of deaths occurred after withdrawal of life support. ARDS patients were more likely to have pulmonary dysfunction as the primary cause of death and die while requiring significant respiratory support compared to patients without ARDS.
hUMSC transplantation restores ovarian function in POI rats by inhibiting autophagy of theca-interstitial cells via the AMPK/mTOR signaling pathway
Authors: Lu Xueyan , Bao Hongchu , Cui Linlu , Zhu Wenqian , Zhang Lianshuang , Xu Zheng , Man Xuejing , Chu Yongli , Fu Qiang , Zhang Hongqin 
Published: July 2020

Abstract
Background
Previous studies of primary ovarian insufficiency (POI) have focused on granulosa cells (GCs) and ignored the role of theca-interstitial cells (TICs). This study aims to explore the mechanism of the protective effects of human umbilical cord-derived mesenchymal stem cells (hUMSCs) on ovarian function in POI rats by regulating autophagy of TICs.

Methods
The POI model was established in rats treated with cisplatin (CDDP). The hUMSCs were transplanted into POI rats by tail vein. Enzyme-linked immunosorbent assay (ELISA) analysis, hematoxylin and eosin (HE) staining, and immunohistochemistry were used to measure the protective effects of hUMSCs. The molecular mechanisms of injury and repairment of TICs were assessed by immunofluorescence, transmission electron microscope (TEM), flow cytometry (FCM), western blot, and quantitative real-time polymerase chain reaction (qRT-PCR).

Results
In vivo, hUMSC transplantation restored the ovarian function and alleviated the apoptosis of TICs in POI rats. In vitro, hUMSCs reduced the autophagy levels of TICs by reducing oxidative stress and regulating AMPK/mTOR signaling pathway, thereby alleviating the apoptosis of TICs.

Conclusion
This study indicates that hUMSCs protected ovarian function in POI by regulating autophagy signaling pathway AMPK/mTOR.
Reduction in depressive symptoms predicts improvement in eating disorder symptoms in interpersonal psychotherapy: results from a naturalistic study
Authors: Bäck Malin , Falkenström Fredrik , Gustafsson Sanna Aila , Andersson Gerhard , Holmqvist Rolf 
Published: July 2020

AbstractBackgroundInterpersonal psychotherapy (IPT) can be effective for both Bulimia Nervosa (BN) and co-occurring depression. While changes in symptoms of Eating disorder (ED) and depression have been found to correlate, it is unclear how they interact during treatment and in which order the symptoms decrease.MethodsThirty-one patients with BN and depressive symptoms received IPT using the manual IPT-BNm in a naturalistic design. The outcome was measured with the Eating Disorder Examination Questionnaire (EDE-Q) and the Montgomery Åsberg Depression Rating Scale (MADRS-S). Symptom improvement at each session was measured with Repeated Evaluation of Eating Disorder Symptoms (REDS) and the Patient Health Questionnaire-9 (PHQ-9).ResultsSignificant improvements with large effect sizes were found on both ED symptoms and depression. The rates of change were linear for both BN and depression. A strong correlation between reduction of depressive symptoms and ED symptoms was found. Depressive symptom reduction at one session predicted improvement of ED symptoms at the next session.ConclusionsIPT-BNm had an effect on both BN and co-occurring depressive symptoms. The analyses indicated that reduction in depressive symptoms preceded reduction in bulimic symptoms.
Long-term survival after hepatectomy for metachronous liver metastasis of pancreatic ductal adenocarcinoma: a case report
Authors: Tsutsumi Chikanori , Abe Toshiya , Shinkawa Tomohiko , Nishihara Kazuyoshi , Tamiya Sadafumi , Nakano Toru 
Published: July 2020

Abstract
Background
Pancreatic ductal adenocarcinoma (PDAC) is among the most aggressive malignancies. The prognosis for recurrence after surgery is extremely unfavorable, and liver metastasis of PDAC confers poor prognosis despite resection.

Case presentation
A 51-year-old man was admitted to our hospital for further examination and treatment, including surgery for a pancreatic tumor. On close inspection, he was suspected to have pancreatic head cancer without enlarged lymph nodes or distant metastasis, and pancreatoduodenectomy with D2 lymph node dissection was performed. A postoperative pathological examination revealed well-differentiated invasive ductal adenocarcinoma with lymph node metastasis (stage IIB; pT2N1M0). Postoperatively, he received adjuvant chemotherapy containing gemcitabine for 1 year. Eight years after the radical surgery, his serum carbohydrate antigen 19-9 level was elevated, and computed tomography (CT) and magnetic resonance imaging revealed a well-circumscribed 10-mm mass in liver segment 5. Positron emission tomography/CT also revealed high fluorine-18-fluorodeoxyglucose uptake only in this hepatic tumor. Accordingly, the patient was diagnosed with a solitary liver metastasis of PDAC. As the liver metastasis was isolated and identified long after the initial surgery, we decided to resect it using laparoscopic partial hepatectomy of segment 5. Histopathological examination confirmed liver metastasis of PDAC and the patient received adjuvant chemotherapy containing S-1. No evidence of recurrence has been seen for 11 years since the pancreatoduodenectomy and 3 years since the hepatic resection.

Conclusions
Cases of metachronous liver metastasis of PDAC after radical surgery, in which patients exhibit long-term survival without recurrence after hepatectomy, are extremely rare. Hepatectomy may confer long-term survival, and the time to postoperative recurrence and the number of liver metastases may be useful criteria for deciding whether to perform hepatic resection.
An extremely rare case of rapidly growing mediastinal well-differentiated liposarcoma with a sclerosing variant: a case report
Authors: Iwamoto Naoya , Matsuura Yosuke , Ninomiya Hironori , Ichinose Junji , Nakao Masayuki , Ishikawa Yuichi , Okumura Sakae , Mun Mingyon 
Published: July 2020

Abstract
Background
Liposarcoma arising from the mediastinum is rare, accounting for less than 1% of mediastinal tumors. Furthermore, a rapidly growing well-differentiated liposarcoma is extremely rare. A well-differentiated liposarcoma is usually considered a low-grade malignancy. However, we present an extremely rare case of a sclerosing variant of well-differentiated liposarcoma that grew rapidly within a year.

Case presentation
A 77-year-old man with a giant mass in the left thoracic cavity was referred to our hospital. This mass measured about 10 cm and occupied the left-sided mediastinum on a chest radiography; however, there was no abnormal finding on the previous year’s chest radiography. Chest-enhanced computed tomography revealed a well-circumscribed 11-cm mass in the left-sided anterior mediastinum. Positron emission tomography showed accumulation of fluorodeoxyglucose uptake in this tumor (maximum standard uptake value = 3.3). The radiological findings of computed tomography and positron emission tomography indicated that this tumor was a benign or low-grade malignancy; therefore, the chest radiographic findings were difficult to explain. To explain this discrepancy and establish the diagnosis, tumor resection was performed via left posterolateral thoracotomy. Intraoperatively, the left phrenic nerve and pericardium were adhered tightly to the tumor, so we resected them. The tumor was well-circumscribed and fibrous; therefore, the initial diagnosis was solitary fibrous tumor. However, based on its histopathological and immunohistochemical patterns, the tumor was diagnosed as a sclerosing variant of well-differentiated liposarcoma. Five years postoperatively, the patient remains alive with no evidence of disease recurrence.

Conclusions
A well-differentiated liposarcoma is usually considered a low-grade malignancy. Nevertheless, the giant tumor in the present case appeared within 1 year. Thus, this was an extremely rare case of a sclerosing variant of well-differentiated liposarcoma with rapid growth.
Aberrant expression for microRNA is potential crucial factors of haemorrhoid
Authors: Song Chengkun , Zhou Haikun , Lu Hong , Luo Chunsheng , Wang Chen , Wang Qingming , Peng Yunhua , Xin Yaojie , Liu Te , Yang Wei 
Published: July 2020

Abstract
Background
Haemorrhoids occur commonly and frequently in the human digestive system. There are diverse causes of haemorrhoids and their in-depth pathogenesis is still currently unclear.

Methods
In this study, we explored haemorrhoids from an epigenetics perspective by employing RNA-Seq for comprehensive and in-depth analysis of the differences in microRNA (miRNA) transcripts between haemorrhoidal tissue and normal tissue in 48 patients with Grade II and above haemorrhoids.

Results
The results showed that 9 miRNAs were significantly upregulated (ratio > 3.5 and P-value < 0.01) and 16 miRNAs were significantly downregulated (ratio > 0.6 and P-value < 0.01) in haemorrhoid tissue. Subsequently, target gene prediction results showed that there were 184 potential target genes of significantly upregulated miRNAs (common to both TargetScan7.1 and MirdbV5 databases) and there were 372 potential target genes of significantly downregulated miRNAs. Gene ontology analysis results showed that the target genes of differentially expressed miRNAs in haemorrhoids are involved in regulating “cell composition” and “protein binding”. Lastly, KEGG search found that the differentially expressed miRNAs that are associated with the occurrence of haemorrhoids mainly regulate the activity of endocytosis and the synaptic vesicle cycle.

Conclusions
In summary, the results of high-throughput RNA-Seq screening suggested that the occurrence of haemorrhoids may be intimately associated with aberrant miRNA transcription, resulting in aberrant target gene expression and an imbalance in certain signal transduction pathways.