bluuebunny/crossref_metadata_2025_split huggingface dataset:
Establishment of a novel culture method for maintaining intestinal stem cells derived from human induced pluripotent stem cells
Authors: Kondo Satoshi , Mizuno Shota , Hashita Tadahiro , Iwao Takahiro , Matsunaga Tamihide 
Published: January 2020

ABSTRACT
The small intestine plays an important role in the pharmacokinetics of orally administered drugs due to the presence of drug transporters and drug-metabolizing enzymes. However, few appropriate methods exist to investigate intestinal pharmacokinetics. Induced pluripotent stem (iPS) cells can form various types of cells and represent a potentially useful tool for drug discovery. We previously reported that differentiated enterocytes from human iPS cells are useful for pharmacokinetic studies; however, the process is time and resource intensive. Here, we established a new two-dimensional culture method for maintaining human iPS-cell-derived intestinal stem cells (ISCs) with differentiation potency and evaluated their ability to differentiate into enterocytes exhibiting appropriate pharmacokinetic function. The culture method used several factors to activate signalling pathways required for maintaining stemness, followed by differentiation into enterocytes. Functional evaluation was carried out to verify epithelial-marker expression and inducibility and activity of metabolic enzymes and transporters. Our results confirmed the establishment of an ISC culture method for maintaining stemness and verified that the differentiated enterocytes from the maintained ISCs demonstrated proper pharmacokinetic function. Thus, our findings describe a time- and cost-effective approach that can be used as a general evaluation tool for evaluating intestinal pharmacokinetics.
Enhancer transcription identifies cis-regulatory elements for photoreceptor cell types
Authors: Perez-Cervantes Carlos , Smith Linsin A. , Nadadur Rangarajan D. , Hughes Andrew E. O. , Wang Sui , Corbo Joseph C. , Cepko Constance , Lonfat Nicolas , Moskowitz Ivan P. 
Published: January 2020

ABSTRACT
Identification of cell type-specific cis-regulatory elements (CREs) is crucial for understanding development and disease, although identification of functional regulatory elements remains challenging. We hypothesized that context-specific CREs could be identified by context-specific non-coding RNA (ncRNA) profiling, based on the observation that active CREs produce ncRNAs. We applied ncRNA profiling to identify rod and cone photoreceptor CREs from wild-type and mutant mouse retinas, defined by presence or absence, respectively, of the rod-specific transcription factor (TF) Nrl. Nrl-dependent ncRNA expression strongly correlated with epigenetic profiles of rod and cone photoreceptors, identified thousands of candidate rod- and cone-specific CREs, and identified motifs for rod- and cone-specific TFs. Colocalization of NRL and the retinal TF CRX correlated with rod-specific ncRNA expression, whereas CRX alone favored cone-specific ncRNA expression, providing quantitative evidence that heterotypic TF interactions distinguish cell type-specific CRE activity. We validated the activity of novel Nrl-dependent ncRNA-defined CREs in developing cones. This work supports differential ncRNA profiling as a platform for the identification of cell type-specific CREs and the discovery of molecular mechanisms underlying TF-dependent CRE activity.
DNA interference by a mesophilic Argonaute protein, CbcAgo
Authors: García-Quintans Nieves , Bowden Laurie , Berenguer José , Mencía Mario 
Published: January 2020

Background: The search for putative enzymes that can facilitate gene editing has recently focused its attention on Argonaute proteins from prokaryotes (pAgos). Though they are structural homologues of human Argonaute protein, which uses RNA guides to interfere with RNA targets, pAgos use ssDNA guides to identify and, in many cases, cut a complementary DNA target. Thermophilic pAgos from Thermus thermophilus, Pyrococcus furiosus and Methanocaldococcus jasmanii have been identified and thoroughly studied, but their thermoactivity makes them of little use in mesophilic systems such as mammalian cells. Methods: Here we search for and identify CbcAgo, a prokaryotic Argonaute protein from a mesophilic bacterium, and characterize in vitro its DNA interference activity. Results: CbcAgo efficiently uses 5’P-ssDNA guides as small as 11-mers to cut ssDNA targets, requires divalent cations (preferentially, Mn2+) and has a maximum activity between 37 and 42 °C, remaining active up to 55 °C. Nicking activity on supercoiled dsDNA was shown. However, no efficient double-strand breaking activity could be demonstrated. Conclusions: CbcAgo can use gDNA guides as small as 11 nucleotides long to cut complementary ssDNA targets at 37ºC, making it a promising starting point for the development of new gene editing tools for mammalian cells.
Paediatric morbidity and mortality in Sierra Leone. Have things changed after the 2014/2015 Ebola outbreak?
Authors: Sesay Tom , Denisiuk Olga , Zachariah Rony 
Published: January 2020

Background: Sierra Leone was severely affected by the 2014/2015 Ebola outbreak which is likely to have had longer term repercussions on the health system including on paediatric morbidity and mortality. We thus assessed under-five morbidity and mortality for malaria, acute respiratory Infections (ARI)/pneumonia, watery diarrhoea and measles during the post-Ebola period in Sierra Leone and compared this with the pre- and intra-Ebola periods. Methods: This was a retrospective cross-sectional study using program data from the District Health Information system (DHIS2) and sourced from 14 districts in Sierra Leone. It included under-five children from 1,250 health facilities country-wide. Study periods included: before (June 1 st, 2013-April 30 th, 2014); during (June 1 st, 2014-April 30 th, 2015); and after Ebola (June 1 st, 2016-April 30 th, 2017). Results: Malaria, ARI/pneumonia and diarrhoea consultations declined during Ebola but recovered to pre-Ebola levels in the post-Ebola period. During the post-Ebola period, there was a highly significant reduction in case-fatality for the first three morbidities compared to the pre-Ebola period (P<0.0001). Average number of measles cases increased from 48/month in the pre-Ebola period to 568/month (12-fold increase) post-Ebola. Although there was no difference in measles case-fatality between the pre- and post-Ebola periods, case-fatality post-Ebola was significantly lower than during Ebola (Relative Risk: 0.05, 95% confidence interval 0.02-0.15, P<0.0001). Conclusions: Consultations for under-five children at health facilities in Sierra Leone recovered to pre-Ebola levels and case-fatality for common childhood illnesses declined significantly. This is a change for the better. However, the high level of reported measles cases in the post-Ebola period indicates gaps in immune status and needs focused attention.
Staffing in public health facilities after the Ebola outbreak in rural Sierra Leone: How much has changed?
Authors: Squire James Sylvester , Hann Katrina , Denisiuk Olga , Zachariah Rony 
Published: January 2020

Background:The 2014-2015 Ebola outbreak in Sierra Leone led the Ministry of Health and Sanitation to set minimum standards of staffing (medical/non-medical) at the district level for the provision of basic essential health services (BPEHS).In one of the worst Ebola affected districts in Sierra Leone, we assessed staffing levels measured against these stipulated standards before, during, and 16 months after the Ebola outbreak.Methods:The study population included all health workers in 83 health facilities. We assessed staffing levels at three points in time: pre-Ebola (April 2014); the end of the outbreak (November 2015); and 16 months post-Ebola (March 2017).April 2014 was immediately prior to the Ebola outbreak and thus representative of the human resource situation before the outbreak. November 2015 was the month when Sierra Leone was declared Ebola-free, and thus reflects the end-situation after Ebola. March 2017 was two years since the launch of the BPEHS, and some progress should be expected.Results:Against recommended medical staff numbers during pre-, intra- and post-Ebola periods, deficits were 67%, 65% and 60% respectively. Similarly, against recommended non-medical staff numbers during pre-, intra- and post-Ebola periods, the deficit remained at 92% throughout. In the post-Ebola period, there was a deficit of 73% against 1,389 recommended health worker positions.Conclusions:Nothing has really changedin the state of human resources for health, and urgent measures are needed to rectify the situation and prevent adéjà vuin the advent of a new Ebola outbreak.
Applying inter-rater reliability to improve consistency in classifying PhD career outcomes
Authors: Stayart C. Abigail , Brandt Patrick D. , Brown Abigail M. , Dahl Tamara , Layton Rebekah L. , Petrie Kimberly A. , Flores-Kim Emma N. , Peña Christopher G. , Fuhrmann Cynthia N. , Monsalve Gabriela C. 
Published: January 2020

Background: There has been a groundswell of national support for transparent tracking and dissemination of PhD career outcomes. In 2017, individuals from multiple institutions and professional organizations met to create the Unified Career Outcomes Taxonomy (UCOT 2017), a three-tiered taxonomy to help institutions uniformly classify career outcomes of PhD graduates. Early adopters of UCOT 2017, noted ambiguity in some categories of the career taxonomy, raising questions about its consistent application within and across institutions. Methods: To test and evaluate the consistency of UCOT 2017, we calculated inter-rater reliability across two rounds of iterative refinement of the career taxonomy, classifying over 800 PhD alumni records via nine coders. Results: We identified areas of discordance in the taxonomy, and progressively refined UCOT 2017 and an accompanying Guidance Document to improve inter-rater reliability across all three tiers of the career taxonomy. However, differing interpretations of the classifications, especially for faculty classifications in the third tier, resulted in continued discordance among the coders. We addressed this discordance with clarifying language in the Guidance Document, and proposed the addition of a flag system for identification of the title, rank, and prefix of faculty members. This labeling system provides the additional benefit of highlighting the granularity and the intersectionality of faculty job functions, while maintaining the ability to sort by - and report data on - faculty and postdoctoral trainee roles, as is required by some national and federal reporting guidelines. We provide specific crosswalk guidance for how a user may choose to incorporate our suggestions while maintaining the ability to report in accordance with UCOT 2017. Conclusions: Our findings underscore the importance of detailed guidance documents, coder training, and periodic collaborative review of career outcomes taxonomies as PhD careers evolve in the global workforce. Implications for coder-training and use of novice coders are also discussed.
Case Report: Pseudoxanthoma elasticum
Authors: Lucas Catarina , Aranha João , da Rocha Isabel , Sousa Domingos 
Published: January 2020

Pseudoxanthoma elasticum (PXE) is a rare inherited disorder, characterised by a progressive mineralization and fragmentation of elastic fibres of the skin, retina and cardiovascular system. At an initial stage, the skin usually exhibits distinctive lesions and subsequently extra-dermal manifestations. The diagnosis is based on clinical manifestations, histological analysis of the lesions and genetic analysis. This is a case report of a 12-year-old child complaining of painless, mildly itchy yellow papules in the cervical region with 1 year of evolution. PXE is currently an incurable disease and has a favourable prognosis when cardiovascular and retinal complications are prevented and monitored.
THE EFFECTS OF TYPICAL THORIUM IMPURITIES ON THORIUM-BASED NUCLEAR FUELS
Authors: Alexander Jude S. , Edwards Geoffrey W.R. , Bromley Blair P. , Lane Keira 
Published: January 2020

Natural thorium contains impurities of numerous isotopes. A study was performed to examine the influence of naturally occurring impurities in thorium-based fuels on a few parameters of interest such as: exit burnup, coolant void reactivity (CVR), fuel temperature coefficients (FTC), and the radiotoxicity of the used fuel. Two different fuel bundle designs were modeled: a 43-element bundle containing 2.25% U-233, and a 35-element bundle containing 1.45% U-233. Naturally occurring thorium fuel impurities were applied to both fuel bundle models at various concentrations, from 0% to 100% of the expected maximum. For burnup-averaged k-infinity (k∞) values of 1.050 and 1.030, exit burnup, burnup-weighted CVR, and burnup-weighted FTC were calculated using the neutron transport code WIMS-AECL, and plotted against fraction of full impurity concentration to determine how the impurity levels affect these reactor physics parameters of interest. For the most-realistic (for CANDU) burnup-averaged k∞ of 1.050, both the inhalation radiotoxicity and the production of U-232 were calculated using the fuel depletion code WOBI. Up to the maximum impurity concentrations considered, no effects on the investigated fuel performance parameters were found to be greater than a few percent.
Primiparous women's narratives of confidence in the perinatal period
Authors: Khajehei Marjan , Swain Julie Ann , Wen Yuhang 
Published: January 2020

BackgroundPregnancy and childbirth are described as transitional phases or existential thresholds that childbearing women have to cross.AimTo gather insights into the personal experiences of women in pregnancy, labour and the days immediately after birth.MethodsWe conducted a qualitative study in the postpartum ward at Westmead Hospital. We invited 16 primiparous women who had given birth to a single baby to participate in our study. After the participants signed the consent form, we conducted individual, in-depth interviews. We analysed the data using thematic analysis.FindingsConfidence was an overarching theme that contributed to the women's experiences of pregnancy, labour and the immediate days after birth. The experiences encompassed two main categories: positive experiences that aided in building confidence, and negative experiences that adversely affected women's confidence. The themes relating to positive experiences, including effective interpersonal relationships, knowledge promotion and positive self-concept, made the women feel more confident. The themes relating to negative experiences, including lack of control and feeling unprepared, made the women feel less confident in their mothering capabilities.ConclusionConfidence was the overarching theme in this study and knowledge was shown to be the fundamental feature of confidence.
SAFER: A mnemonic to improve safety-netting advice
Authors: Silverston Paul 
Published: January 2020

Paul Silverston describes a mnemonic to help facilitate the development of symptom-based, patient safety-focused, safety-netting advice In primary care, patients often present during the early stages of an illness, before the findings required to establish the correct diagnosis have developed. This creates the potential for both diagnostic uncertainty and diagnostic error. There is also the possibility that a patient diagnosed with a minor illness may subsequently develop an uncommon but serious complication of that illness. Patients must be made aware of these risks and given advice as to when they should seek a medical re-assessment of their symptoms. This is referred to as safety-netting advice. Patients and relatives need to know the specific symptoms and signs to check for and the criteria that would mandate the need for a re-assessment. It is essential that safety-netting advice is patient-centred and that the medical content of that advice is symptom-based and patient safety-focused. This article describes a mnemonic, SAFER, which can be used to improve the quality of the safety-netting advice given to patients.
The development of coffee cultivation in the traditional agroforestry of mixed-garden (dukuh lembur) to provide social-economic benefit for the Outer Baduy Community, South Banten, Indonesia
Authors: BUDIWATI S. ISKANDAR  , JOHAN ISKANDAR  , BUDI IRAWAN  , SUROSO  , Partasasmita Ruhyat 
Published: January 2020

Abstract. Iskandar BS, Iskandar J, Irawan I, Suroso, Pasratasmita R. 2019. The development of coffee cultivation in the traditional agroforestry of mixed-garden (dukuh lembur) to provide social-economic benefit for the Outer Baduy Community, South Banten, Indonesia. Biodiversitas 20: 2958-2969. The Baduy community who resides in the Village of Kanekes, the Sub-district of Leuwidamar, the District of Lebak, South Banten has maintained the Sundanese tradition, particularly in practicing swidden farming (ngahuma). They practice swidden farming based on Traditional Ecological Knowledge (TEK) and belief. According to the Baduy tradition, the commercial plants, including coffee, clove, cacao, teak, and rubber have been prohibited to cultivate in Baduy area. However, because the population has increased rapidly and market economy has intensively penetrated the Baduy area, some commercial plants, including robusta coffee (Coffea canephora Pierre ex A. Froehner) have been introduced by the outer Baduy community. The objective of this study was to elucidate the traditional practice of the Outer Baduy in cultivating coffee trees that are integrated into the traditional agroforestry of mixed-garden (dukuh lembur or leuweung lembur). This study used qualitative method with some techniques of collecting data, including observation, participant observation, semi-structured interviews, and plant survey in the sample plots of the dukuh lembur. The results of the study showed that in 1980-s the robusta coffee plants were introduced by some Outer Baduy people and have since been planted in the dukuh lembur. In the past, because coffee was prohibited to be cultivated in Baduy area, the coffee trees were regularly cut during the purification of the Baduy tradition (pembersihan adat). Nowadays, however, the robusta coffee trees have been properly integrated into the existing dukuh lembur which is based on hybrid knowledge of TEK and scientific Western knowledge. The Outer Baduy coffee farming system has provided subsistence as a well commercial economy that may support the sustainability of the Outer Baduy swidden cultivation that is considered as the cultural identity of the Baduy community.
Diagnosis of electrically active defects in CH3NH3PbI3 perovskite solar cells via admittance spectroscopy measurements
Authors: Xue Juanjuan , Hu Xiaobo , Guo YiXin , Weng Guoen , Jiang Jinchun , Chen Shaoqiang , Zhu Ziqiang , Chu Junhao 
Published: January 2020

The defect properties of

C
H

3

N
H

3

P
b
I

3

solar cells with efficiencies ranging from 7.70% to 12.51% were investigated using admittance spectroscopy measurements. Trap levels of the same kind with activation energies varied in the range of 0.16–0.23 eV above the valence band were found for different samples and identified as an interface-type defect. Moreover, the defect parameters, including the capture cross section of the holes, capture lifetime of the holes, and defect density, were extracted, and their relationships with the cell efficiencies were investigated. The results indicated that, compared with other parameters, defect density is a critical factor for

C
H

3

N
H

3

P
b
I

3

solar cell performance.
Enhanced responsivity of co-hyperdoped silicon photodetectors fabricated by femtosecond laser irradiation in a mixed SF6/NF3 atmosphere
Authors: Ma Sheng-Xiang , Liu Xiao-Long , Sun Hai-Bin , Zhao Yang , Hu Yue , Ning Xi-Jing , Zhao Li , Zhuang Jun 
Published: January 2020

Co-hyperdoped silicon is fabricated on single crystalline Si substrate by using femtosecond-laser pulses in a mixed gas of

S
F

6

and

N
F

3

with different ratios. With the increase of the proportion of

N
F

3

in the mixed gas, the co-hyperdoped silicon shows increased crystallinity but decreased sub-bandgap absorption. Photodetectors are fabricated based on these samples without high-temperature thermal annealing. With the increase of the proportion of

N
F

3

, the photoelectric response first increases and then decreases. Photodetectors based on the co-hyperdoped (

N
F

3

/

S
F

6

, 35/35 kPa) material without high-temperature thermal annealing demonstrate high performance on photoresponsivity (

6

A

W

−
1

@

−
5

V

for 1050 nm), which is an order of magnitude higher compared with the photodetector made from S-hyperdoped silicon. The photoconductive gain accounts for the high responsivity.
Observation of PT-symmetry in a fiber ring laser
Authors: Fan Zhiqiang , Zhang Weifeng , Qiu Qi , Yao Jianping 
Published: January 2020

A wavelength-tunable single-mode laser with a sub-kilohertz linewidth based on parity-time (PT)-symmetry is proposed and experimentally demonstrated. The proposed PT-symmetric laser is implemented based on a hybrid use of an optical fiber loop and a thermally tunable integrated microdisk resonator (MDR). The MDR, implemented based on the silicon-on-insulator, operates with the optical fiber loop to form two mutually coupled cavities with an identical geometry. By controlling two light waves passing through the two cavities, with one having a gain coefficient and the other a loss coefficient but with an identical magnitude, a PT-symmetric laser is implemented. Thanks to an ultranarrow passband of the cavity due to PT-symmetry, single-longitudinal mode lasing is achieved. The tuning of the wavelength is implemented by thermally tuning the MDR. The proposed PT-symmetric laser is demonstrated experimentally. Single-longitudinal mode lasing at a wavelength of around 1555 nm with a sub-kilohertz linewidth of 433 Hz is implemented. The lasing wavelength is continuously tunable from 1555.135 to 1555.887 nm with a tuning slope of 75.24 pm/°C.
Thermal-induced luminescence enhancement of BAC-P in bismuth-doped phosphogermanosilicate fibers
Authors: Zhao Qiancheng , Hao Qun , Luo Yanhua , Peng Gang-Ding 
Published: January 2020

The thermal quenching effect has been systematically investigated in bismuth (Bi)-doped phosphogermanosilicate fiber with varying thermal conditions. For the first time, to the best of our knowledge, the activation of phosphor-related Bi active center (BAC-P) is achieved by thermal quenching at 400°C with a heating time of 10 min, evidenced by the enhanced luminescence of BAC-P (

∼

1.3

times) at 1300 nm. The experimental results reveal that a relatively low heating temperature with prolonged heating time stimulates the growth of BAC-P, whereas higher operating temperatures (

≥

500
∘

C) result in the irreversible destruction of BAC-P. The underlying mechanism for the thermally stimulated BAC-P process is also analyzed and discussed.
Facilitated tip-enhanced Raman scattering by focused gap-plasmon hybridization
Authors: Chen Houkai , Zhang Yuquan , Dai Yanmeng , Min Changjun , Zhu Siwei , Yuan Xiaocong 
Published: January 2020

Tip-enhanced Raman scattering (TERS) spectroscopy is a nondestructive and label-free molecular detection approach that provides high sensitivity and nanoscale spatial resolution. Therefore, it has been used in a wide array of applications. We demonstrate a gap-plasmon hybridization facilitated by a bottom-illuminated TERS configuration. The gap-plasmon hybridization effect is first performed with the finite-difference time-domain method to optimize the parameters, and experiments are then conducted to calibrate the performance. The results demonstrate an enhancement factor of 1157 and a spatial resolution of 13.5 nm. The proposed configuration shows great potential in related surface imaging applications in various fields of research.