bluuebunny/crossref_metadata_2025_split huggingface dataset:
Maximum likelihood estimation for randomized shortest paths with trajectory data
Authors: Kivimäki Ilkka , Van Moorter Bram , Panzacchi Manuela , Saramäki Jari , Saerens Marco 
Published: July 2020

AbstractRandomized shortest paths (RSPs) are tool developed in recent years for different graph and network analysis applications, such as modelling movement or flow in networks. In essence, the RSP framework considers the temperature-dependent Gibbs–Boltzmann distribution over paths in the network. At low temperatures, the distribution focuses solely on the shortest or least-cost paths, while with increasing temperature, the distribution spreads over random walks on the network. Many relevant quantities can be computed conveniently from this distribution, and these often generalize traditional network measures in a sensible way. However, when modelling real phenomena with RSPs, one needs a principled way of estimating the parameters from data. In this work, we develop methods for computing the maximum likelihood estimate of the model parameters, with focus on the temperature parameter, when modelling phenomena based on movement, flow or spreading processes. We test the validity of the derived methods with trajectories generated on artificial networks as well as with real data on the movement of wild reindeer in a geographic landscape, used for estimating the degree of randomness in the movement of the animals. These examples demonstrate the attractiveness of the RSP framework as a generic model to be used in diverse applications.
Language and the National Past in Napoleonic France: Reassessing the Académie celtique, 1805–1813
Authors: Stewart Ian B 
Published: July 2020

Abstract
This article reassesses the Académie celtique (1805–13), an antiquarian society concerned with investigating the origins of the French nation, and the progenitor of the current Société nationale des antiquaires de France. While most prior scholarship has focused on the Académie as an innovator in the field of French folklore studies, it is argued here that the Académie’s main scholarly concern was with language, specifically the use of historical linguistic research for tracing the origins of European nations. Underpinning the Académie’s research programme was a belief that the ancient Celts—based in Gaul—once dominated Europe and spoke a language from which most European tongues descended, and was perhaps preserved in modern Breton. The article therefore also presents a coherent view of the importance of Celtic ancestry for the developing French nation in the early nineteenth century.
Upregulation of PD-L1 expression promotes epithelial-to-mesenchymal transition in sorafenib-resistant hepatocellular carcinoma cells
Authors: Xu Gui-Li , Ni Cai-Fang , Liang Han-Si , Xu Yun-Hua , Wang Wan-Sheng , Shen Jian , Li Ming-Ming , Zhu Xiao-Li 
Published: July 2020

Abstract

Background
The epithelial-to-mesenchymal transition (EMT) status is associated with programmed death-1 ligand 1 (PD-L1) expression in various cancers. However, the role and molecular mechanism of PD-L1 in the EMT of sorafenib-resistant hepatocellular carcinoma (HCC) cells remain elusive. In this study, we aimed to investigate the regulation of PD-L1 on the EMT in sorafenib-resistant HCC cells.

Methods
Initially, the sorafenib-resistant HCC cell lines HepG2 SR and Huh7 SR were established. Western-blot assays were used to detect the expression of PD-L1, E-cadherin, and N-cadherin. The intervention and overexpression of PD-L1 were used to explore the role of PD-L1 in the regulation of EMT in HepG2 SR and Huh7 SR cells. Cell migration and invasion were assessed by transwell assays. PD-L1 or Sterol regulatory element-binding protein 1 (SREBP-1) overexpression and knock-down were performed in order to study the mechanism of PD-L1 in sorafenib-resistant HCC cells.

Results
PD-L1 expression was upregulated, whereas E-cadherin levels were downregulated and N-cadherin expression was increased in HepG2 SR and Huh7 SR cells. The cell viabilities of HepG2 and Huh7 cells were lower than those of HepG2 SR and Huh7 SR cells. PD-L1 overexpression reduced E-cadherin expression and increased N-cadherin levels, whereas PD-L1 knock-down increased E-cadherin expression and decreased N-cadherin expression. PD-L1 expression promoted EMT and the migratory and invasive abilities of HepG2 SR and Huh7 SR cells. PD-L1 promoted the EMT of sorafenib-resistant HCC cells via the PI3K/Akt pathway by activating SREBP-1 expression in HepG2 SR and Huh7 SR cells.

Conclusions
The findings reveal that PD-L1 expression promotes EMT of sorafenib-resistant HCC cells.
Loneliness as a Biographical Disruption—Theoretical Implications for Understanding Changes in Loneliness
Authors: Morgan Deborah J , Burholt Vanessa 
Published: July 2020

Abstract

Objectives
While a great deal is known about the risk factors that increase vulnerability to loneliness in later life, little research has explored stability and change in levels of loneliness.

Methods
Narrative interviews were conducted with 11 participants who were identified as being lonely during Wave 1 of the Maintaining Function and Well-being in Later Life Study Wales (CFAS Wales). The interviews were used to explore stability and change in levels of loneliness from the perspective of older people themselves. The interviews focused on participant’s perspectives of the events that triggered loneliness, stability, and change in levels of loneliness over time as well as participant’s responses to loneliness.

Results
The findings show that participants experienced losses and loneliness as biographical disruption. How participants and their wider social network responded to these losses had implications for the individual’s trajectory through loneliness.

Discussion
Drawing on a biographical lens, the study reframed the events that triggered loneliness as disruptive events. This article discusses the utility of biographical disruption in understanding stability and change in loneliness. The findings suggest how drawing on valued identities may help lonely adults transition out of loneliness.
Assessment of fecal DNA extraction protocols for metagenomic studies
Authors: Yang Fangming , Sun Jihua , Luo Huainian , Ren Huahui , Zhou Hongcheng , Lin Yuxiang , Han Mo , Chen Bing , Liao Hailong , Brix Susanne , Li Junhua , Yang Huanming , Kristiansen Karsten , Zhong Huanzi 
Published: July 2020

Abstract

Background
Shotgun metagenomic sequencing has improved our understanding of the human gut microbiota. Various DNA extraction methods have been compared to find protocols that robustly and most accurately reflect the original microbial community structures. However, these recommendations can be further refined by considering the time and cost demands in dealing with samples from very large human cohorts. Additionally, fungal DNA extraction performance has so far been little investigated.

Results
We compared 6 DNA extraction protocols, MagPure Fast Stool DNA KF Kit B, Macherey Nagel™ NucleoSpin™®Soil kit, Zymo Research Quick-DNA™ Fecal/Soil Microbe kit, MOBIO DNeasy PowerSoil kit, the manual non-commercial protocol MetaHIT, and the recently published protocol Q using 1 microbial mock community (MMC) (containing 8 bacterial and 2 fungal strains) and fecal samples. All samples were manually extracted and subjected to shotgun metagenomics sequencing. Extracting DNA revealed high reproducibility within all 6 protocols, but microbial extraction efficiencies varied. The MMC results demonstrated that bead size was a determining factor for fungal and bacterial DNA yields. In human fecal samples, the MagPure bacterial extraction performed as well as the standardized protocol Q but was faster and more cost-effective. Extraction using the PowerSoil protocol resulted in a significantly higher ratio of gram-negative to gram-positive bacteria than other protocols, which might contribute to reported gut microbial differences between healthy adults.

Conclusions
We emphasize the importance of bead size selection for bacterial and fungal DNA extraction. More importantly, the performance of the novel protocol MP matched that of the recommended standardized protocol Q but consumed less time, was more cost-effective, and is recommended for further large-scale human gut metagenomic studies.
How does firm innovation size affect the timing of technology licensing? Theory and evidence from China
Authors: Ma Rongkang , Zhu Shanshan , Liu Fengchao 
Published: July 2020

Abstract
Previous research has highlighted the importance of firm size for the propensity of technology licensing. However, the currently available knowledge regarding how firm innovation size affects the timing of technology licensing is limited, especially in developing economies such as that of China. Therefore, in the context of the Chinese patent system, this article builds a model for the timing decision of technology licensing from the perspective of licensors. This model theoretically reveals the relationship between firm innovation size and the likelihood of technology licensing at different time points. This article argues that there is a positive relationship between firm innovation size and the likelihood of technology licensing before the patent disclosure date; moreover, there is an inverted U-shaped relationship between the firm innovation size and the likelihood of licensing between the patent disclosure date and the grant date; however, firm innovation size is negatively correlated with the likelihood of licensing after the patent grant date. Empirical results based on 8737 first-time licensing data on invention patents of Chinese firms in 2001–2015 support all predictions. This study contributes to both the scholarly understanding of timing decision making in firms’ technology licensing and the design of technology transfer policies for different firms in China.
Near Real-Time Identification of Recent Human Immunodeficiency Virus Transmissions, Transmitted Drug Resistance Mutations, and Transmission Networks by Multiplexed Primer ID–Next-Generation Sequencing in North Carolina
Authors: Zhou Shuntai , Sizemore Sabrina , Moeser Matt , Zimmerman Scott , Samoff Erika , Mobley Victoria , Frost Simon , Cressman Andy , Clark Michael , Skelly Tara , Kelkar Hemant , Veluvolu Umadevi , Jones Corbin , Eron Joseph , Cohen Myron , Nelson Julie A E , Swanstrom Ronald , Dennis Ann M 
Published: July 2020

Abstract

Background
The identification of recent human immunodeficiency virus (HIV) 1 infections among people with new HIV diagnoses is important to both tailoring and assessing the impact of HIV-1 prevention strategies.

Methods
We developed a multiplexed Primer ID–next-generation sequencing approach to identify recent infections by measuring the intrahost viral diversity over multiple regions of the HIV-1 genome, in addition to detecting drug resistance mutations (DRMs) and phylogenetically linked clusters. We summarize the field implementation of this all-in-one platform among persons with newly diagnosed HIV-1 by the North Carolina State Laboratory of Public Health in 2018.

Results
Overall, recent infection was identified in 94 (35%) of 268 patients with new HIV diagnoses. People &lt;30 years old, and people who inject drugs were more likely to have diagnoses of recent infection. The reverse-transcriptase region K103N was the most commonly detected DRM (prevalence, approximately 15%). We found a total of 28 clusters, and persons with recent infection were more likely to be cluster members than were those with chronic infections (P = .03).

Conclusions
We demonstrate the rapid identification of recent infection and pretreatment DRMs coupled with cluster analysis that will allow prioritization of linkage to care, treatment, and prevention interventions to those at highest risk of onward transmission.
The apparent ileal digestibility and the apparent total tract digestibility of carbohydrates and energy in hybrid rye are different from some other cereal grains when fed to growing pigs
Authors: McGhee Molly L , Stein Hans H 
Published: July 2020

AbstractAn experiment was conducted to determine the apparent ileal digestibility (AID) and the apparent total tract digestibility (ATTD) of energy, starch, and total dietary fiber (TDF) in two varieties of hybrid rye and compare these values with values obtained for barley, wheat, corn, and sorghum. It was hypothesized that there are no differences in AID and ATTD of energy and nutrients among hybrid rye, barley, wheat, and sorghum. Twenty-four ileal cannulated barrows (initial body weight = 28.1 ± 3.0 kg) were randomly allotted to a two-period experimental design with six diets and four replicate pigs in each period for a total of eight replicate pigs per diet. Diets consisted of 97% of each grain, and each pig received a different diet in each period. The initial 5 d of each period were considered the adaptation period, whereas urine and fecal materials were collected from the feed provided from day 6 to 10, and ileal digesta were collected on days 12 and 13 of each period. Results indicated that the metabolizable energy (ME) on a dry matter (DM) basis was greatest (P &lt; 0.05) in corn and wheat (3,732 and 3,641 kcal/kg DM), and least (P &lt; 0.05) in barley (3,342 kcal/kg DM), whereas the two hybrid ryes contained 3,499 and 3,459 kcal/kg DM, respectively. The ME values in hybrid rye were not different from values determined for barley and sorghum (3,573 kcal/kg DM). In all grains, the AID of starch was greater than 90%, and the ATTD of starch was nearly 100%. Barley contained more TDF than the other cereal grains, and the two hybrid ryes had concentrations of soluble dietary fiber that were close to the concentration in barley but greater than in wheat, corn, and sorghum. The AID of TDF was less than 35% for all cereal grains, but the ATTD of TDF was greater (P &lt; 0.05) in the two hybrid ryes (68% and 70%) than in the other ingredients (56% to 58%). In conclusion, feeding hybrid rye to pigs resulted in reduced pre-cecal absorption of energy compared with wheat, corn, and sorghum, but because hindgut fermentation of fiber was greater in hybrid rye than in other cereal grains, the content of ME in hybrid rye was not different from barley and sorghum but less than in corn and wheat.
Method for Postmortem Tissue Quantification of Δ9-Tetrahydrocannabinol and Metabolites Using LC–MS-MS
Authors: Al-Asmari Ahmed I 
Published: July 2020

Abstract
A method for analyzing Δ9-tetrahydrocannabinol (THC), 11-hydroxy-Δ9-THC (THC-OH) and 11-nor-Δ9-THC-9-carboxylic acid (THC-COOH) in postmortem solid specimens using liquid chromatography–tandem mass spectrometry was developed and validated. A Stomacher instrument was used to prepare these tissues before extraction. Prior to solid phase extraction, liver, kidney, stomach, lung, brain, muscle, bladder and intestine tissues were pretreated with alkaline hydrolysis. All calibration curves were found to be linear with coefficients of determination greater than 0.99. The limit of quantification was 1.0 ng/g. Using three controls, within-run precision ranged between 1.0 and 12.0%, between-run precision ranged between 1.0 and 6.0%, and accuracy ranged between −7.0 and 8.0%. Matrix effects ranged from −21 to 24%. After matrix effects were excluded, analytical recoveries ranged from 79 to 97%. The distributions of THC, THC-OH and THC-COOH were investigated in 32 postmortem cases that tested positive for cannabinoids. This revealed new information regarding the distribution of THC metabolites in stomach, intestine and bladder. Alkaline hydrolysis was sufficient for the deglucuronidation of THC-COOH-glucuronide to its free form, THC-COOH, in all tissues of interest. In conclusion, measuring THC and its metabolites (THC-OH and THC-COOH) in tissues is crucial for any forensic toxicology detection method, especially when bodies are heavily decomposed, as solid tissues may be the only specimens available for testing.
The Impact of a Comprehensive Risk Prediction Model for Colorectal Cancer on a Population Screening Program
Authors: Saya Sibel , Emery Jon D , Dowty James G , McIntosh Jennifer G , Winship Ingrid M , Jenkins Mark A 
Published: July 2020

Abstract

Background
In many countries, population colorectal cancer (CRC) screening is based on age and family history, though more precise risk prediction could better target screening. We examined the impact of a CRC risk prediction model (incorporating age, sex, lifestyle, genomic, and family history factors) to target screening under several feasible screening scenarios.

Methods
We estimated the model’s predicted CRC risk distribution in the Australian population. Predicted CRC risks were categorized into screening recommendations under 3 proposed scenarios to compare with current recommendations: 1) highly tailored, 2) 3 risk categories, and 3) 4 sex-specific risk categories. Under each scenario, for 35- to 74-year-olds, we calculated the number of CRC screens by immunochemical fecal occult blood testing (iFOBT) and colonoscopy and the proportion of predicted CRCs over 10 years in each screening group.

Results
Currently, 1.1% of 35- to 74-year-olds are recommended screening colonoscopy and 56.2% iFOBT, and 5.7% and 83.2% of CRCs over 10 years were predicted to occur in these groups, respectively. For the scenarios, 1) colonoscopy was recommended to 8.1% and iFOBT to 37.5%, with 36.1% and 50.1% of CRCs in each group; 2) colonoscopy was recommended to 2.4% and iFOBT to 56.0%, with 13.2% and 76.9% of cancers in each group; and 3) colonoscopy was recommended to 5.0% and iFOBT to 54.2%, with 24.5% and 66.5% of cancers in each group.

Conclusions
A highly tailored CRC screening scenario results in many fewer screens but more cancers in those unscreened. Category-based scenarios may provide a good balance between number of screens and cancers detected and are simpler to implement.
Raltegravir-associated Drug-Reaction With Eosinophilia and Systemic Symptoms Syndrome in a Pediatric Patient Without Characteristic Human Leukocyte Antigen B*57:01 or B*53:01 alleles
Authors: Thomas Sanya J , Kilgore Jacob T , Becken Bradford A , Cunningham Coleen K , Thompson Amelia B 
Published: July 2020

Abstract
We present the first published case of raltegravir-associated drug-reaction with eosinophilia and systemic symptoms (DRESS) syndrome in a child without characteristic human leukocyte antigen haplotypes HLA-B*57:01 or HLA-B*53:01. A 4-year-old African American female with perinatally acquired human immunodeficiency virus infection was hospitalized for DRESS after starting a raltegravir-based antiretroviral regimen.
Laparoscopic assisted submucosal excision of an intussuscepting colonic lipoma
Authors: Ejtehadi Farshid , Mohammed Elsamoual , Vijay Vardhini 
Published: July 2020

Abstract
Colonic lipomas are the most widespread non-epithelial tumours of the large bowel. They often present with absent, non-specific or intermittent symptoms. Intussusception is the most common complication that may occur as a result of such a lesion. We present the case of a young female patient with a history of intermittent abdominal pain associated with nausea. She presented to the emergency department with subacute large bowel obstruction. A diagnosis of colo-colic intussusception due to a large descending colonic lipoma was confirmed on CT scan. The patient underwent a laparoscopic assisted submucosal excision of the lipoma. We discuss this unique operative technique as well as preoperative investigations and histopathology findings. Although successful endoscopic excision of lipomas has been reported, segmental resection of the colon is most commonly practiced. To the best of our knowledge, this is the first report of laparoscopic assisted submucosal excision of an intussuscepting colonic lipoma.
‘The Being that is in a Manner Equal with God’ (Phil. 2:6C): A Self-Transforming, Incarnational, Divine Ontology
Authors: Fletcher-Louis Crispin 
Published: July 2020

Abstract
This article challenges the consensus that τὸ εἶναι ἴσα θεῷ (Phil. 2:6c) means ‘equality with God’ and denotes a status. Linguistic analysis, contextual considerations, and a thorough investigation of an inventory of 149 extant Greek references to divine equality (ἴσος /ἴσα + θεός) show that Phil. 2:6c means ‘being (that is) in a manner equal with God’. Although it evokes well-known language for the status of rulers who received ‘honours equal to the gods’, it has a distinct, rarely attested, but Homeric syntax (cf. Iliad 5:441–2; 21:315), for which the closest parallel is Homeric Hymns 5, line 214. As such, it denotes a dynamic ontology, a mode of being expressed, or actualized, in Christ’s incarnational self-transformation (vv. 7–8). The words also serve a creative affirmation and subversion of the middle Platonic distinction between ‘being’ and ‘becoming’ (as that was expressed in Plutarch and Philo): Christ exists and acts from ‘being’ (ὑπάρχων … τὸ εἶναι v. 6) and is misperceived in the realm of ‘becoming’ (γενόμενος … γενόμενος vv. 7–8). But, against the Platonists, he has a divine ‘being’ that ‘becomes’.
Reorganisation of rhizosphere soil pore structure by wild plant species in compacted soils
Authors: Burr-Hersey Jasmine E , Ritz Karl , Bengough Glyn A , Mooney Sacha J 
Published: July 2020

Abstract
Soil compaction represents a major impediment to plant growth, yet wild plants are often observed thriving in soil of high bulk density in non-agricultural settings. We analysed the root growth of three non-cultivated species often found growing in compacted soils in the natural environment. Plants of ribwort plantain (Plantago lanceolata), dandelion (Taraxacum officinale), and spear thistle (Cirsium vulgare) were grown for 28 d in a sandy loam soil compacted to 1.8 g cm–3 with a penetration resistance of 1.55 MPa. X-Ray computed tomography was used to observe root architecture in situ and to visualise changes in rhizosphere porosity (at a resolution of 35 μm) at 14 d and 28 d after sowing. Porosity of the soil was analysed within four incremental zones up to 420 μm from the root surface. In all species, the porosity of the rhizosphere was greatest closest to the root and decreased with distance from the root surface. There were significant differences in rhizosphere porosity between the three species, with Cirsium plants exhibiting the greatest structural genesis across all rhizosphere zones. This creation of pore space indicates that plants can self-remediate compacted soil via localised structural reorganisation in the rhizosphere, which has potential functional implications for both plant and soil.