bluuebunny/crossref_metadata_2025_split huggingface dataset:
A comparative study of aged and contemporary Chinese herbal materials by using delayed luminescence technique
Authors: Jia Yusheng , Sun Mengmeng , Shi Yuhua , Zhu Zhihui , van Wijk Eduard , van Wijk Roeland , van Andel Tinde , Wang Mei 
Published: January 2020

AbstractBackgroundInvestigation of aged Chinese herbal materials will help us to understand their use and sources in ancient time and broaden the historical perspective of Chinese material medica. To reach this aim, the basic understanding of aged herbal materials, including physical and chemical characters, is of great importance. Delayed luminescence (DL) technique was developed as a rapid, direct, systemic, objective and sample loss-free tool to characterize the properties of Chinese herbal materials. In this study, we measured DL values in aged Chinese herbal materials that were transported from Asia to Europe during the 20th century and stored in Naturalis Biodiversity Center and the Utrecht University museum, and compared these with modern material of the same species.MethodsA hyperbolic function was used to extract four properties from the DL curves of Chinese herbal material from 1900, the 1950s and recently harvested products. Statistical tools, including the Student’s t test, One-way analysis of variance and Principal Component Analysis, were used to differentiate the DL properties of aged and contemporary collections ofGlycyrrhizaspp.Curcuma aromaticaSalisb.,Zingiber officinaleRoscoe,Alpinia officinarumHance andAcorus calamusL.ResultsOur results showed that DL properties were significantly different between historical and contemporary Chinese herbal materials. Changes in DL values were species-dependent: the effects of storage time of DL properties were specific for each species. These outcomes help us not only in the identification of historical Chinese medicine products but also provides valuable data of the effect of storage time on herbal materials.ConclusionThe simple, direct, rapid, and inexpensive measurements offered by DL provide a novel tool to assess the taxonomic identity of Chinese and other herbal materials and assess the differences in chemical properties with increasing storage time. Our results contribute to the further development of novel digital tools for the quality control of herbal materials.
Nationwide carrier detection and molecular characterization of β-thalassemia and hemoglobin E variants in Bangladeshi population
Authors: Noor Farjana Akther , Sultana Nusrat , Bhuyan Golam Sarower , Islam Md Tarikul , Hossain Mohabbat , Sarker Suprovath Kumar , Islam Khaleda , Khan Waqar Ahmed , Rahman Mujahida , Qadri Syeda Kashfi , Shekhar Hossain Uddin , Qadri Firdausi , Qadri Syed Saleheen , Mannoor Kaiissar 
Published: January 2020

Abstract
Background
ß-thalassemia is one of the most common inherited blood disorders in the world and a major deterrent to the public health of Bangladesh. The management of thalassemia patients requires lifelong frequent blood transfusion and the available treatment options are unsatisfactory. A national policy on thalassemia prevention is mandatory in Bangladesh. However, precise and up-to-date information on the frequency of ß-thalassemia carriers are missing due to lack of accurate diagnostic approaches, limited access to information and absence of national screening program. This study aims to determine the nationwide carrier frequency of hemoglobin E (HbE) and β- thalassemia and mutation spectrum among the carriers using molecular, hematological and biochemical methods.

Methods
The study enrolled a total of 1877 individuals (60.1% male and 39.9% female) aged between 18 and 35 years. Total sample size and its division-wise breakdown were calculated in proportion to national and division-wise population. Venous blood was collected and subjected to CBC analysis and Hb-electrophoresis for each participant. Serum ferritin was measured to detect coexistence of iron deficiency anemia with thalassemia carrier. DNA-based High Resolution Melting (HRM) curve analysis was performed for confirmation of carrier status by mutation detection.

Results
Of 11.89% (95% CI, 10.43–13.35) carriers of β-globin gene mutations, 8.68% (95% CI, 7.41–9.95) had HbE trait (ETT) and 2.24% (95% CI, 1.57–2.91) had beta-thalassemia trait (BTT). Among eight divisions, Rangpur had the highest carrier frequency of 27.1% (ETT-25%, BTT-2.1%), whereas Khulna had the lowest frequency of 4.2% (ETT-4.2% only). Moreover, α- thalassemia, HbD trait, HbE disease, hereditary persistence of HbF were detected in 0.11, 0.16, 0.43 and 0.16% participants, respectively. HRM could identify two individuals with reported pathogenic mutations in both alleles who were erroneously interpreted as carriers by hematological indices. Finally, a total of nine different mutations including a novel mutation (c.151A > G) were detected in the β-globin gene.

Conclusions
Since carrier frequency for both HbE and β-thalassemia is alarmingly high in Bangladesh, a nationwide awareness and prevention program should be made mandatory to halt the current deteriorating situations. Mutation-based confirmation is highly recommended for the inconclusive cases with conventional carrier screening methods to avoid any faulty detection of thalassemia carriers.
Diverse approaches to predicting drug-induced liver injury using gene-expression profiles
Authors: Sumsion G. Rex , Bradshaw Michael S. , Beales Jeremy T. , Ford Emi , Caryotakis Griffin R. G. , Garrett Daniel J. , LeBaron Emily D. , Nwosu Ifeanyichukwu O. , Piccolo Stephen R. 
Published: January 2020

AbstractBackgroundDrug-induced liver injury (DILI) is a serious concern during drug development and the treatment of human disease. The ability to accurately predict DILI risk could yield significant improvements in drug attrition rates during drug development, in drug withdrawal rates, and in treatment outcomes. In this paper, we outline our approach to predicting DILI risk using gene-expression data from Build 02 of the Connectivity Map (CMap) as part of the 2018 Critical Assessment of Massive Data Analysis CMap Drug Safety Challenge.ResultsFirst, we used seven classification algorithms independently to predict DILI based on gene-expression values for two cell lines. Similar to what other challenge participants observed, none of these algorithms predicted liver injury on a consistent basis with high accuracy. In an attempt to improve accuracy, we aggregated predictions for six of the algorithms (excluding one that had performed exceptionally poorly) using a soft-voting method. This approach also failed to generalize well to the test set. We investigated alternative approaches—including a multi-sample normalization method, dimensionality-reduction techniques, a class-weighting scheme, and expanding the number of hyperparameter combinations used as inputs to the soft-voting method. We met limited success with each of these solutions.ConclusionsWe conclude that alternative methods and/or datasets will be necessary to effectively predict DILI in patients based on RNA expression levels in cell lines.ReviewersThis article was reviewed by Paweł P Labaj and Aleksandra Gruca (both nominated by David P Kreil).
De novo variants in exomes of congenital heart disease patients identify risk genes and pathways
Authors: Sevim Bayrak Cigdem , Zhang Peng , Tristani-Firouzi Martin , Gelb Bruce D. , Itan Yuval 
Published: January 2020

Abstract
Background
Congenital heart disease (CHD) affects ~ 1% of live births and is the most common birth defect. Although the genetic contribution to the CHD has been long suspected, it has only been well established recently. De novo variants are estimated to contribute to approximately 8% of sporadic CHD.

Methods
CHD is genetically heterogeneous, making pathway enrichment analysis an effective approach to explore and statistically validate CHD-associated genes. In this study, we performed novel gene and pathway enrichment analyses of high-impact de novo variants in the recently published whole-exome sequencing (WES) data generated from a cohort of CHD 2645 parent-offspring trios to identify new CHD-causing candidate genes and mutations. We performed rigorous variant- and gene-level filtrations to identify potentially damaging variants, followed by enrichment analyses and gene prioritization.

Results
Our analyses revealed 23 novel genes that are likely to cause CHD, including HSP90AA1, ROCK2, IQGAP1, and CHD4, and sharing biological functions, pathways, molecular interactions, and properties with known CHD-causing genes.

Conclusions
Ultimately, these findings suggest novel genes that are likely to be contributing to CHD pathogenesis.
Transcriptomic profiling disclosed the role of DNA methylation and histone modifications in tumor-infiltrating myeloid-derived suppressor cell subsets in colorectal cancer
Authors: Sasidharan Nair Varun , Saleh Reem , Toor Salman M. , Taha Rowaida Z. , Ahmed Ayman A. , Kurer Mohamed A. , Murshed Khaled , Alajez Nehad M. , Abu Nada Mohamed , Elkord Eyad 
Published: January 2020

AbstractBackgroundIncreased numbers of myeloid-derived suppressor cells (MDSCs) are positively correlated with poor prognosis and reduced survivals of cancer patients. They play central roles in tumor immune evasion and tumor metastasis. However, limited data are available on phenotypic/transcriptomic characteristics of the different MDSCs subsets in cancer. These cells include immature (I-MDSCs), monocytic (M-MDSCs), and polymorphonuclear/granulocytic (PMN-MDSCs).MethodsPhenotypic characterization of myeloid subsets from 27 colorectal cancer (CRC) patients was assessed by flow cytometric analyses. RNA-sequencing of sorted I-MDSCs, PMN-MDSCs, and antigen-presenting cells (APCs) was also performed.ResultsWe found that the levels of I-MDSCs and PMN-MDSCs were increased in tumor tissues (TT), compared with normal tissues (NT) in colorectal cancer. Our functional annotation analyses showed that genes associated with histone deacetylase (HDAC) activation- and DNA methylation-mediated transcriptional silencing were upregulated, and histone acetyl transferase (HAT)-related genes were downregulated in tumor-infiltrating I-MDSCs. Moreover, pathways implicated in cell trafficking and immune suppression, including Wnt, interleukin-6 (IL-6), and mitogen-activated protein kinase (MAPK) signaling, were upregulated in I-MDSCs. Notably, PMN-MDSCs showed downregulation in genes related to DNA methylation and HDAC binding. Using an ex vivo model, we found that inhibition of HDAC activation or neutralization of IL-6 in CRC tumor tissues downregulates the expression of genes associated with immunosuppression and myeloid cell chemotaxis, confirming the importance of HDAC activation and IL-6 signaling pathway in MDSC function and chemotaxis.ConclusionsThis study provides novel insights into the epigenetic regulations and other molecular pathways in different myeloid cell subsets within the CRC tumor microenvironment (TME), giving opportunities to potential targets for therapeutic benefits.
The challenge of combining variable retention and prescribed burning in Finland
Authors: Lindberg Henrik , Punttila Pekka , Vanha-Majamaa Ilkka 
Published: January 2020

AbstractHistorically, wildfires have played an important role in forest dynamics in Fennoscandia. In Finland, the annually burned area has diminished in recent decades. This has led to a decline of fire-adapted habitat types and species, many of which have become red-listed. In Fennoscandia, there is a long tradition of silvicultural burnings to enhance tree regeneration. Recently, prescribed burnings have been modified for biodiversity goals following the recommendations that have emerged from ecological research. Prominent biodiversity gains can be obtained by combining sufficient retention levels with burnings. Consequently, burning and retention have been recommended by recent national red-list assessments, strategies, and forest-management guidelines, and they have been adopted in forest-certification standards in Finland. Contrary to these recommendations, the opposite development has taken place: (1) the ecological efficiency of the criterion concerning prescribed burning in the PEFC forest-certification standard has been impaired, (2) state funding to encourage private forest owners to apply prescribed burning was reduced significantly, and (3) prescribed burnings have been abandoned altogether in commercial state-owned forests. Traditional burnings with variable retention have also been partially replaced with burning of small retention-tree groups. This new method is less risky and cheaper, but its ecological benefits are questionable because small-sized fires produce much smaller areas of burned forest soil with less fire-affected wood than traditional silvicultural burnings. Generally, the widely accepted goal to increase burnings with retention appears difficult to achieve and would require stronger political will and economic support from the government. We identified several actions that could improve the weakened situation of fire-dependent biodiversity and recommend the following: (1) setting a clear goal and ensuring sufficient funding for the burnings—including restoration burnings in conservation areas—and targeting these to specific fire-continuum areas with sufficient retention to ensure the continuity of fire-affected habitats at landscape level; (2) renewing the current subsidizing policies to encourage private landowners to perform prescribed burnings in regeneration areas after final fellings, and to safeguard accidental forest-fire areas as set-asides; (3) renewing the current prescribed-burning criterion of the Finnish PEFC forest-certification standard with more ambitious ecological goals; and (4) re-introducing prescribed burnings in commercial state forests where management targets are under political steering.
Effects of bio-loggers on behaviour and corticosterone metabolites of Northern Bald Ibises (Geronticus eremita) in the field and in captivity
Authors: Puehringer-Sturmayr Verena , Loretto Matthias-Claudio A. , Hemetsberger Josef , Czerny Tanja , Gschwandegger Johannes , Leitsberger Madelaine , Kotrschal Kurt , Frigerio Didone 
Published: January 2020

AbstractBackgroundDuring the past decades, avian studies have profited from the development of miniature electronic devices that allow long-term and long-range monitoring. To ensure data quality and to inform understanding of possible impacts, it is necessary to test the effects of tagging. We investigated the influence of GPS-transmitters on the behaviour and physiology (levels of excreted corticosterone metabolites, CM) of an endangered bird species, the Northern Bald Ibis (Geronticus eremita). We considered effects of GPS-tags in two contexts: (1) aviary (i.e. in captivity), focussing on short-term effects of transmitters on locomotion, foraging and maintenance behaviour (20 individuals that differed in sex and age observed for 10 days) and (2) field, focussing on intermediate-term effects of transmitters on locomotion, foraging, maintenance behaviour, dorsal feather preening, social interactions and physiology (CM) (24 individuals observed for 79 days). In both contexts, focal animals were equipped with bio-logger backpacks mounted with a harness.ResultsIn the aviary, behavioural observations were limited to the first days after tagging: no differences were found between individuals with GPS-tags and their controls with respect to the behavioural parameters considered. In the field, no behavioural differences were found between the GPS-tagged individuals and their controls; however, 1 month after tagging, individuals with GPS-tags excreted significantly more CM than their controls before returning to baseline levels.ConclusionsOur results suggest that GPS-transmitters did not affect foraging, locomotion and maintenance behaviour in the Northern Bald Ibis in the short- or intermediate-term. However, they did affect the hypothalamic–pituitary–adrenal reactivity in the intermediate-term for 1 month before returning to baseline levels the next month. As the Northern Bald Ibis is listed as endangered, evaluating possible adverse effects of bio-logging is also relevant for potential conservation and reintroduction research.
Single-drill implant induces bone corticalization during submerged healing: an in vivo pilot study
Authors: Trisi Paolo , Falco Antonello , Berardini Marco 
Published: January 2020

AbstractPurposeThe aim of the present paper is to evaluate a simplified implant site preparation technique to preserve bone bulk and enhance osseointegration using a new conical self-tapping implant in cancellous bone.Materials and methodsTen Expander® 3.8 × 10 mm implants (NoDrill®, Milano, Italy) were inserted in the right side (test group) of sheep’s iliac crest using only the pilot drill 1.8 mm in diameter. Ten 3.8 × 10 mm Dynamix® implants (Cortex, Shlomi, Israel) were inserted in the right side (control group) of the same animals following the drilling protocol provided by the manufacturer. Histological, histomorphometric, and biomechanical analyses were performed after 2 months.ResultsImplants that belonged to the test group showed a %BIC of 70.91 ± 7.95 while the control group implants had a %BIC value of 49.33 ± 10.73. The %BV was 41.83 ± 6.30 in the test group and 29.61 ± 5.05 in the control group. These differences were statistically significant. A phenomenon of osseocorticalization, characterized by more bone volume percentage around implant area than in the neighboring areas, caused by implant threads geometry, was evident in the test group.ConclusionThis surgical protocol allows to insert an innovative fixture geometry in low-density bone using only a pilot drill. This technique demonstrated many clinical and histological advantages with respect to standard implant drilling procedures and classical implant geometry.
Group status, geographic location, and the tone of media coverage: Jews and Muslims in New York Times and Guardian Headlines, 1985–2014
Authors: Nisar Hasher , Bleich Erik 
Published: January 2020

AbstractStudies demonstrate that both group status and geographic location influence media coverage of immigrants, ethnic groups, and marginalized communities. We examine a systematic sample of headlines about Muslims and Jews from The New York Times and The Guardian between 1985 and 2014 to understand these two factors. We find that headlines about Jews have a more positive tone than those about Muslims, and that headlines about each group situated within the newspaper’s country—such as American Jews or British Muslims—have a more positive tone than those set in the Middle East and North Africa (MENA) region—such as MENA Jews or MENA Muslims. These findings provide independent confirmation of prevailing research on group status and on the differences between coverage of domestic and foreign events. We expand this research agenda by intersecting these two strands of scholarship to examine the interaction between group status and geographic location, comparing the tone of headlines about lower-status domestic groups—such as Muslims in the United States or Great Britain—to that of the higher-status foreign group of Jews in the MENA region. We find that there is no meaningful difference between the portrayal of American Muslims and MENA Jews in The New York Times, but that Guardian headlines are significantly more positive toward British Muslims compared to MENA Jews. We explore these cross-national differences to show how the relationship between group status and geography is context specific.
Live birth rate after IVF/ICSI in women with low and extremely low AMH: an age-matched controlled study
Authors: Zaghloul Yomna I. , Amin Yahia M. , Mansour Ragaa T. , Serour Ahmed , Aboulghar Mona M. , Aboulghar Mohamed A. , Serour Gamal I. 
Published: January 2020

Abstract
Background
An age-matched controlled study, to assess the outcome of IVF/ICSI in low and extremely low AMH levels in different age groups by comparing the live birth rate

Materials and methods
An age-matched controlled study was done at the Egyptian IVF center, Cairo, Egypt, including 306 infertile women with low AMH levels undergoing IVF/ICSI and an age-matched number of women with normal AMH. The live birth rate in the different age groups according to the AMH level was compared.

Results
There was no significant difference between LBR in the extremely low AMH arm (11.43%) and low AMH (16.4%) (P = 0.24). The LBR was 30.4% in women with normal AMH as compared to 14.7% in all women with AMH below 1 pg/ml (P = 0.002).
The LBR was significantly higher in women below the age of 35 years and women of 35-40 years with normal AMH (33.2% and 31.7%) as compared to LBR in the corresponding age groups with low AMH (18.6% and 13.3%).

Conclusions
There was no difference in the outcome of IVF between patients with low and extremely low AMH levels. Women with normal AMH level resulted in a higher pregnancy rate as compared to women with low AMH level in the same age group. Age is important in determining prognosis of IVF in patients with low levels of AMH.
Helical tomotherapy with a complete-directional-complete block technique effectively reduces cardiac and lung dose for left-sided breast cancer
Authors: Yeh Hsin-Pei , Huang Yu-Chuen , Wang Li-Ying , Shueng Pei-Wei , Tien Hui-Ju , Chang Chiu-Han , Chou San-Fang , Hsieh Chen-Hsi 
Published: January 2020

Objectives:
To evaluate the feasibility and optimal restricted angle of the complete-directional-complete block (CDCB) technique in helical tomotherapy (HT) by including regional nodal irradiation (RNI) with the internal mammary node (IMN) in left-sided breast cancer.

Methods:
Ten left-sided breast cancer patients treated with 50 Gy in 25 fractions were compared with five-field intensity-modulated radiation therapy (5F-IMRT) and six types of HT plans. In the HT plans, complete block (CB), organ-based directional block (OBDB) and CDCB with different restricted angles were used.

Results:
The conformity index (CI) between the CDCB0,10,15,20 and 5F-IMRT groups was similar. Compared to CB, OBDB and 5F-IMRT, CDCB20 resulted in a decreased ipsilateral mean lung dose. The low-dose region (V5) of the ipsilateral lung in OBDB (84.0%) was the highest among all techniques (p &lt; 0.001). The mean dose of the heart in CB was significantly reduced (by 11.5–22.4%) compared with other techniques. The V30 of the heart in CDCB20 (1.9%) was significantly lower than that of CB, OBDB and 5F-IMRT. Compared to the mean dose of the left anterior descending (LAD) artery of 5F-IMRT (27.0 Gy), CDCB0, CDCB10, CDCB15, CDCB20 and OBDB reduced the mean dose effectively by 31.7%, 38.3%, 39.6%, 42.0 and 56.2%, respectively. Considering the parameters of the organs-at-risk (OARs), CDCB10,15,20 had higher expectative values than the other techniques (p = 0.01).

Conclusions:
HT with the CDCB technique is feasible for treating left-sided breast cancer patients. The CDCB10-20 techniques not only achieved similar planning target volume coverage, homogeneity and dose conformity but also allowed better sparing of the heart and bilateral lungs.

Advances in knowledge:
For left-sided breast cancer patients whose RNI field includes the IMN, heart avoidance is an important issue. The CDCB technique achieved good PTV coverage, homogeneity and dose conformity and allowed better sparing of the mean dose of the lung, the LAD artery, and the heart and reduced the V30 of the heart.