bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ultradeep targeted sequencing of circulating tumor DNA in plasma of early and advanced breast cancer
Authors: Chin Yoon Ming , Takahashi Yoko , Chan Hiu Ting , Otaki Masumi , Fujishima Makoto , Shibayama Tomoko , Miki Yoshio , Ueno Takayuki , Nakamura Yusuke , Low Siew‐Kee 
Published: October 2020

AbstractWe present a study to evaluate the feasibility and clinical utility of amplicon‐based Oncomine Pan‐Cancer cell‐free assay to detect circulating tumor DNA (ctDNA) in patients with early or advanced breast cancer. In this study, 109 early and metastatic breast cancer patients were recruited before the initiation of treatment. ctDNA mutation profiles were assessed through unique molecular tagging (UMT) and ultradeep next generation sequencing (NGS). For patients with mutations, DNA from corresponding white blood cells (WBC) was sequenced to exclude variants of clonal‐hematopoietic (CH) origin. UMT targeted sequencing from plasma of 109 patients achieved a median total coverage of 55 498X and a median molecular coverage of 4187X. Among 53 ctDNA positive samples, 38% were mutation positive by WBC sequencing, indicating potentially false‐positive results contributed by CH origin. Prevalence of CH‐related mutations was associated with age (P = 7.51 × 10−4). After exclusion of CH mutations, ctDNA detection rates were 37% for local or locally advanced breast cancer (stage I‐III) and 81% for metastatic or recurrent breast cancer. The ctDNA detection rate correlated with disease stage (P = 2.60 × 10−4), nodal spread (P = 6.49 × 10−3) and the status of distant metastases (P = 5.00 × 10−4). ctDNA variants were detected mostly in TP53, PIK3CA and AKT1 genes, with variants showing therapeutic relevance. This pilot study endorses the use of targeted NGS for non‐invasive molecular profiling of breast cancer. Paired sequencing of plasma ctDNA and WBC should be implemented to improve accurate interpretation of liquid biopsy.
N‐pyridinylbenzamides: an isosteric approach towards new antimycobacterial compounds
Authors: Nawrot Daria , Suchánková Eliška , Janďourek Ondřej , Konečná Klára , Bárta Pavel , Doležal Martin , Zitko Jan 
Published: October 2020

AbstractA series of N‐pyridinylbenzamides was designed and prepared to investigate the influence of isosterism and positional isomerism on antimycobacterial activity. Comparison to previously published isosteric N‐pyrazinylbenzamides was made as an attempt to draw structure–activity relationships in such type of compounds. In total, we prepared 44 different compounds, out of which fourteen had minimum inhibitory concentration (MIC) values against Mycobacterium tuberculosis H37Ra below 31.25 µg/ml, most promising being N‐(5‐chloropyridin‐2‐yl)‐3‐(trifluoromethyl)benzamide (23) and N‐(6‐chloropyridin‐2‐yl)‐3‐(trifluoromethyl)benzamide (24) with MIC = 7.81 µg/ml (26 µm). Five compounds showed broad‐spectrum antimycobacterial activity against M. tuberculosis H37Ra, M. smegmatis and M. aurum. N‐(pyridin‐2‐yl)benzamides were generally more active than N‐(pyridin‐3‐yl)benzamides, indicating that N‐1 in the parental structure of N‐pyrazinylbenzamides might be more important for antimycobacterial activity than N‐4. Marginal antibacterial and antifungal activity was observed for title compounds. The hepatotoxicity of title compounds was assessed in vitro on hepatocellular carcinoma cell line HepG2, and they may be considered non‐toxic (22 compounds with IC50 over 200 µm).
Comparing outcomes of children and youth with fetal alcohol spectrum disorder (FASD) in the child welfare system to those in other living situations in Canada: Results from the Canadian National FASD Database
Authors: Burns Jessica , Badry Dorothy E. , Harding Kelly D. , Roberts Nicole , Unsworth Kathy , Cook Jocelynn L. 
Published: October 2020

AbstractAimsThe current study aimed to explore differences in adverse outcomes between youth and adolescents with fetal alcohol spectrum disorder (FASD) living in child welfare care (i.e., foster care or group home) with those living with their biological parent(s) or with adoptive or other family member(s) in Canada.MethodsData gathered from the Canadian National FASD Database were used for analysis. A total of 665 youth and adolescents with a clinical diagnosis of FASD under the age of 18 living in child welfare care, with biological, adoptive or other family members, were included in the sample. Key areas examined included living situation, legal problems, experience of sexual or physical abuse, mental health (anxiety, conduct disorder, mood disorder and post‐traumatic stress disorder) and suicidal ideation. Descriptive statistics and chi‐square comparisons were utilized to explore these differences.ResultsResults revealed a significantly higher rate of reported sexual and physical abuse among individuals in child welfare care compared with those living with biological parents or with adoptive or other family member(s). Rates of difficulty with the law were also higher among those in child welfare care compared with adoptive/other family members. Conversely, the rate of mood disorders was significantly higher among those living with adoptive/other family members compared with child welfare care. Results highlight similar rates of reported suicidal ideation/attempts across all living situations, as well as mental health concerns.ConclusionsResults offer rare insight into the lives of youth and adolescents under age 18 with diagnosed FASD who reside in child welfare care in contrast to those living with biological parent(s) or with adoptive or other family members. These findings increase our awareness of the complexity of mental health concerns and suicide risk across all living environments. Results have further implications for policy, practice and clinical intervention.
Prevalence, concomitant reactions, and factors associated with fragrance allergy in Thailand
Authors: Sukakul Thanisorn , Charoenpipatsin Norramon , Svedman Cecilia , Boonchai Waranya 
Published: October 2020

AbstractBackgroundFragrances are the most common cause of cosmetic contact allergy. Up‐to‐date information on contact allergy frequencies and relevance aids primary and secondary preventive measures.ObjectivesTo determine the prevalence, associated factors, and concomitant reactions in fragrance allergy among Thais.MethodsThis retrospective study collected data from 2012 to 2019. The patient characteristics of fragrance and nonfragrance allergy groups were compared. Concurrent positive reactions to fragrance allergens (fragrance mix [FM] I, FM II, Myroxylon pereirae resin and hydroxyisohexyl 3‐cyclohexene carboxaldehyde) and other baseline‐series allergens were analysed.ResultsOf 1032 patients, 175 (17.0%) had fragrance allergy, with 57.7% of clinical relevance. FM I showed the highest prevalence (9.4%). The associated factors were being elderly, lesions on the extremities, metal allergy history, and long dermatitis duration. Contact allergies to epoxy resin and Compositae plants were significantly associated with fragrance allergy with an odds ratio of 5.95 (95% confidence interval [CI]: 5.21‐6.80) and an odds ratio of 4.42 (95% CI: 1.58‐12.36), respectively. No significant associations between colophonium (previously proposed as a fragrance marker) and fragrance allergens were found.ConclusionsThe prevalence of fragrance contact allergy remains high and should be considered in old patients presenting with long‐standing eczema on the extremities. Unlike reports from other countries, varied, significant, concomitant reactions were observed.
A new approach to flame‐retardant cellulosic fabrics in an environmentally safe manner
Authors: Lewis David M. , Hawkes Jamie A. , Hawkes Liangyu , Mama John 
Published: October 2020

AbstractThis article investigates reacting potassium salts of phosphorous‐containing acids in the presence of urea with cotton cellulose under thermosol conditions (pH 5, 185 °C) to esterify the cellulose and produce a flame‐retardant effect. Attenuated total reflectance‐Fourier‐transform infrared (ATR‐FTIR) spectroscopy confirmed chemical modification of the cotton cellulose, where only the phosphite salt formed a covalently bonded cellulose ester (confirmed by flammability tests). Urea plays a vital role; decomposing to ammonia and isocyanic acid (the reactive intermediate) and it is the isocyanic acid/phosphite anion addition compound that reacts with cellulose hydroxyl groups to form the required ester. ATR‐FTIR analysis showed that phosphate and hypophosphite salts did not react with cellulose and thus gave no flame‐resist effect. Whilst the esterification of cellulose introduces phosphorous onto the cellulose, in order to meet more severe work‐wear laundry standards it was necessary to further incorporate a nitrogen species by addition of a cationic polymer. To develop a one shot “all‐in” process the possibility of simultaneously bonding nitrogen through carbodimide chemistry is researched, with initial promising trials demonstrated. Many after‐treatments of dyed fabrics can cause colour shifts due to interactions with the chromophores. Azo dyes, for example, are particularly susceptible to attack by the formaldehyde produced during the Pyrovatex process or the reducing nature of the Proban process, both resulting in a colour change. An advantage of the novel phosphite/urea flame‐retardant system presented herein, is that the system is less aggressive which allows the possibility of using reactive dyes to produce a bright and wide shade range as the results demonstrate.
Clinical profiles of post‐load glucose subgroups and their association with glycaemic traits over time: An IMI‐DIRECT study
Authors: Obura M. , Beulens J. W. J. , Slieker R. , Koopman A. D. M. , Hoekstra T. , Nijpels G. , Elders P. , Dekker J. M. , Koivula R. W. , Kurbasic A. , Laakso M. , Hansen T. H. , Ridderstråle M. , Hansen T. , Pavo I. , Forgie I. , Jablonka B. , Ruetten H. , Mari A. , McCarthy M. I. , Walker M. , McDonald T. J. , Perry M. H. , Pearson E. R. , Franks P. W. , ‘t Hart L. M. , Rutters F. ,   the IMI‐DIRECT Consortium
Published: October 2020

AbstractAimTo examine the hypothesis that, based on their glucose curves during a seven‐point oral glucose tolerance test, people at elevated type 2 diabetes risk can be divided into subgroups with different clinical profiles at baseline and different degrees of subsequent glycaemic deterioration.MethodsWe included 2126 participants at elevated type 2 diabetes risk from the Diabetes Research on Patient Stratification (IMI‐DIRECT) study. Latent class trajectory analysis was used to identify subgroups from a seven‐point oral glucose tolerance test at baseline and follow‐up. Linear models quantified the associations between the subgroups with glycaemic traits at baseline and 18 months.ResultsAt baseline, we identified four glucose curve subgroups, labelled in order of increasing peak levels as 1–4. Participants in Subgroups 2–4, were more likely to have higher insulin resistance (homeostatic model assessment) and a lower Matsuda index, than those in Subgroup 1. Overall, participants in Subgroups 3 and 4, had higher glycaemic trait values, with the exception of the Matsuda and insulinogenic indices. At 18 months, change in homeostatic model assessment of insulin resistance was higher in Subgroup 4 (β = 0.36, 95% CI 0.13–0.58), Subgroup 3 (β = 0.30; 95% CI 0.10–0.50) and Subgroup 2 (β = 0.18; 95% CI 0.04–0.32), compared to Subgroup 1. The same was observed for C‐peptide and insulin. Five subgroups were identified at follow‐up, and the majority of participants remained in the same subgroup or progressed to higher peak subgroups after 18 months.ConclusionsUsing data from a frequently sampled oral glucose tolerance test, glucose curve patterns associated with different clinical characteristics and different rates of subsequent glycaemic deterioration can be identified.
Atomic structure of and valine binding to the regulatory ACT domain of the Mycobacterium tuberculosis Rel protein
Authors: Shin Joon , Singal Bharti , Sony Subramanian Manimekalai Malathy , Wei Chen Ming , Ragunathan Priya , Grüber Gerhard 
Published: October 2020

The stringent response, regulated by the bifunctional (p)ppGpp synthetase/hydrolase Rel in mycobacteria, is critical for long‐term survival of the drug‐tolerant dormant state of Mycobacterium tuberculosis. During amino acid starvation, MtRel senses a drop in amino acid concentration and synthesizes the messengers pppGpp and ppGpp, collectively called (p)ppGpp. Here, we investigate the role of the regulatory ‘Aspartokinase, Chorismate mutase and TyrA’ (ACT) domain in MtRel. Using NMR spectroscopy approaches, we report the high‐resolution structure of dimeric MtRel ACT which selectively binds to valine out of all other branched‐chain amino acids tested. A set of MtRel ACT mutants were generated to identify the residues required for maintaining the head‐to‐tail dimer. Through NMR titrations, we determined the crucial residues for binding of valine and show structural rearrangement of the MtRel ACT dimer in the presence of valine. This study suggests the direct involvement of amino acids in (p)ppGpp accumulation mediated by MtRel independent to interactions with stalled ribosomes.DatabaseStructural data are available in the PDB database under the accession number 6LXG.
Phosphorus addition decreases microbial residual contribution to soil organic carbon pool in a tropical coastal forest
Authors: Yuan Ye , Li Yue , Mou Zhijian , Kuang Luhui , Wu Wenjia , Zhang Jing , Wang Faming , Hui Dafeng , Peñuelas Josep , Sardans Jordi , Lambers Hans , Wang Jun , Kuang Yuanwen , Li Zhi’an , Liu Zhanfeng 
Published: October 2020

AbstractThe soil nitrogen (N) and phosphorus (P) availability often constrains soil carbon (C) pool, and elevated N deposition could further intensify soil P limitation, which may affect soil C cycling in these N‐rich and P‐poor ecosystems. Soil microbial residues may not only affect soil organic carbon (SOC) pool but also impact SOC stability through soil aggregation. However, how soil nutrient availability and aggregate fractions affect microbial residues and the microbial residue contribution to SOC is still not well understood. We took advantage of a 10‐year field fertilization experiment to investigate the effects of nutrient additions, soil aggregate fractions, and their interactions on the concentrations of soil microbial residues and their contribution to SOC accumulation in a tropical coastal forest. We found that continuous P addition greatly decreased the concentrations of microbial residues and their contribution to SOC, whereas N addition had no significant effect. The P‐stimulated decreases in microbial residues and their contribution to SOC were presumably due to enhanced recycling of microbial residues via increased activity of residue‐decomposing enzymes. The interactive effects between soil aggregate fraction and nutrient addition were not significant, suggesting a weak role of physical protection by soil aggregates in mediating microbial responses to altered soil nutrient availability. Our data suggest that the mechanisms driving microbial residue responses to increased N and P availability might be different, and the P‐induced decrease in the contribution of microbial residues might be unfavorable for the stability of SOC in N‐rich and P‐poor tropical forests. Such information is critical for understanding the role of tropical forests in the global carbon cycle.
Use of Dementia Assessment Sheet for Community‐based Integrated Care System 8‐items (DASC‐8) for the screening of frailty and components of comprehensive geriatric assessment
Authors: Toyoshima Kenji , Araki Atsushi , Tamura Yoshiaki , Ishikawa Joji , Kodera Remi , Oba Kazuhito , Chiba Yuko , Awata Shuichi 
Published: October 2020

AimWe examined whether the Dementia Assessment Sheet for Community‐based Integrated Care System 8‐items (DASC‐8) is useful for screening frailty and as a comprehensive geriatric assessment (CGA).MethodsOutpatients (N = 431; 269 women; Mage = 78.9 ± 6.8 years) with cardiometabolic disease from a frailty clinic participated. Frailty status was assessed using modified Cardiovascular Health Study criteria, the Clinical Frailty Scale and the Kihon Checklist. Cognition, higher‐level activities of daily living, sarcopenia, physical activities, depression, nutrition, medication adherence, social network and quality of life were assessed as CGA components. We examined the association of DASC‐8 category with frailty or CGA components using multiple logistic regression analyses, adjusted for age and sex.ResultsMost participants (n = 310, 71.9%) were in Category I, 90 (20.9%) were in Category II and 31 (7.1%) were in Category III. There were no significant differences in sex, body mass index, or past medical history, except regarding age or cerebral infarction. Logistic regression analyses showed that, for all definitions of frailty, the odds ratios of frailty significantly increased as category progressed. Cognitive function, higher‐level activities of daily living, handgrip strength, gait speed, physical activities, medication adherence, social network and quality of life decreased as the category increased. Although depressive tendency increased in Category II, there was no significant difference in muscle mass or prevalence of sarcopenia among the categories. Malnutrition was observed in Category III.ConclusionsDASC‐8 category was associated with frailty and several CGA components in older patients with cardiometabolic disease. Geriatr Gerontol Int 2020; 20: 1157–1163.
Feasibility of non‐destructive evaluation for apple crispness based on portable acoustic signal
Authors: Liu Yang , Cai Mingjin , Zhang Wangyou , Feng Wanling , Sun Xingyuan , Zhang Yang , Zhou Hongli 
Published: October 2020

SummaryIn this paper, apple crispness was evaluated by sensory evaluation and compared with non‐destructive measurements of portable acoustic signal to discuss the feasibility of non‐destructive evaluation for apple crispness based on portable acoustic signal. Acoustic eigenvalues from the acoustic signal were processed by time domain and Hilbert–Huang transform (HHT), followed by analysing the correlations with apple crispness that had been evaluated via sensory evaluation. Multiple linear regression (MLR) and artificial neural network (ANN) were applied to predict apple crispness. The results proved that crispness correlates significantly (P < 0.01) with four acoustic eigenvalues, including waveform index, sound intensity, energy of low frequency and energy of high frequency. The average relative error of apple crispness predicted by ANN was 1.42 ± 1.9%, remarkably lower (P < 0.01) that of MLR (6.79 ± 5.64%), implying that the model predicted by ANN is more accurate than that of MLR.
Comparative analysis and antibacterial properties of thermally sintered apatites with varied processing conditions
Authors: Jahangir Mehnaz Urbee , Islam Farhana , Wong Siew Yee , Jahan Rumana A. , Matin Md Abdul , Li Xu , Arafat M. Tarik 
Published: October 2020

AbstractHydroxyapatite (HA) and biphasic hydroxyapatite/beta‐tricalcium phosphate (biphasic HA/β‐TCP) were synthesized using thermal sintering. The parameters‐ sintering temperature (600°C, 900°C, and 1200°C), biological source used (fish bone, egg shells, and fish scales), and soaking time (2, 6, and 10 hours) were permuted to study their effects on the properties of the resultant apatite. Morphological study revealed that the smallest (60 nm) spherical particle and the largest (470 nm) irregular shaped particle were obtained from the fish bone sample sintered at 600°C and at 1200°C respectively. FTIR and XRD results showed that as the sintering temperature is increased, the phase transformation from HA to β‐TCP takes place. Only the final products from fishbone sample at 600°C are pure carbonated HA. The crystallinity of synthesized particles ranged from 79% to 98%. Soaking time has no effect on phase composition of the apatite but has significant effect on crystallite size; increase in soaking time increases crystallite size and particle shape becomes more spherical. Interestingly, the fish bone sample sintered at 900°C has higher crystallinity and crystallite size compared to the fish scale sample sintered at the same temperature. EDX confirmed that non‐stoichiometric apatite with Ca/P ratio ranging from 1.47 to 1.91 can be obtained by varying the sintering conditions. The antibacterial test revealed that both calcium apatite obtained from fish bones and fish scales have inhibited bacterial growth; apatite from fish bone works faster than fish scales. The in vitro cytotoxicity test ensured that all the calcium apatite except for eggshell are non‐cytotoxic. Thus, apatite with excellent microbial activity can be obtained by using fish wastes, and by tuning the sintering parameters, the apatite with desired types and properties can be synthesized for different biomedical applications.
Exploiting differences in the energy budget among C4 subtypes to improve crop productivity
Authors: Yin Xinyou , Struik Paul C. 
Published: October 2020

SummaryC4 crops of agricultural importance all belong to the NADP‐malic enzyme (ME) subtype, and this subtype has been the template for C4 introductions into C3 crops, like rice, to improve their productivity. However, the ATP cost for the C4 cycle in both NADP‐ME and NAD‐ME subtypes accounts for > 40% of the total ATP requirement for CO2 assimilation. These high ATP costs, and the associated need for intense cyclic electron transport and low intrinsic quantum yield , are major constraints in realizing strong improvements of canopy photosynthesis and crop productivity. Based on mathematical modelling, we propose a C4 ideotype that utilizes low chloroplastic ATP requirements present in the nondomesticated phosphoenolpyruvate carboxykinase (PEP‐CK) subtype. The ideotype is a mixed form of NAD(P)‐ME and PEP‐CK types, requires no cyclic electron transport under low irradiances, and its theoretical is c. 25% higher than that of a C4 crop type. Its cell‐type‐specific ATP and NADPH requirements can be fulfilled by local energy production. The ideotype is projected to have c. 10% yield advantage over NADP‐ME‐type crops and > 50% advantage over C3 counterparts. The ideotype provides a unique (theoretical) case where could be improved, thereby paving a new avenue for improving photosynthesis in both C3 and C4 crops.
Comment on “Olley and Pakes‐style Production Function Estimators with Firm Fixed Effects”*
Authors: Ackerberg Daniel A. 
Published: October 2020

AbstractIn this comment I illustrate that in the model of (Lee et al. (2019). Oxford Bulletin of Economics and Statistics. Vol. 81, pp. 80–97), firm profit maximizing implies that Assumption 2 and Equation 14 may be contradictory. More specifically, there is generally a contradiction when investment is used as the control variable, but there is generally not a contradiction when a static input like material input is used as the control variable (both types of control variables are discussed in Lee et al.). While the Lee et al. model and techniques are an interesting way to incorporate fixed effects into Olley and Pakes‐style production function estimators, this observation suggests that their application should be restricted to cases where static inputs are used as control variables.