bluuebunny/crossref_metadata_2025_split huggingface dataset:
Organ responses with daratumumab therapy in previously treated AL amyloidosis
Authors: Chung Alfred , Kaufman Gregory P. , Sidana Surbhi , Eckhert Erik , Schrier Stanley L. , Lafayette Richard A. , Arai Sally , Witteles Ronald M. , Liedtke Michaela 
Published: February 2020

Abstract
Immunoglobulin light chain amyloidosis (AL amyloidosis) involves deposition of abnormally folded light chains into a wide range of tissues causing organ dysfunction, including in the heart and kidney. Daratumumab, a CD38-targeted antibody, has recently demonstrated efficacy in producing hematologic responses in previously treated disease. However, data on survival outcomes and organ responses to daratumumab are lacking. Seventy-two patients with previously treated AL amyloidosis who received daratumumab monotherapy with dexamethasone were retrospectively evaluated. With a median follow-up of 27 months, 2-year overall survival (OS) was 86.9% (median OS, not reached) and 2-year time-to-next treatment or death (TTNT)–free survival was 62% (median TTNT, not reached). Forty of 52 evaluable patients achieved a hematologic response (77%), with &gt;60% of patients achieving a very good partial response or better; median time-to-hematologic response was 1 month. Fifty-seven patients (79%) had cardiac involvement, and 55% of evaluable patients achieved a cardiac response, with a median response time of 3.2 months among responders. Cardiac responses were associated with an improvement in OS, with landmark analysis for cardiac responses at 3 months trending toward statistical significance (100% vs 55% at 30 months, P = .051). Forty-seven patients (65%) had renal involvement, and 52% of evaluable patients achieved a renal response, with a median response time of 6 months among responders; there was no significant difference in OS between renal responders and nonresponders. This study demonstrates that daratumumab is highly effective in the treatment of previously treated AL amyloidosis, and a significant proportion of patients can achieve deep hematologic responses, as well as improvements in organ function.
Severe desaturations increase psychomotor vigilance task-based median reaction time and number of lapses in obstructive sleep apnoea patients
Authors: Kainulainen Samu , Duce Brett , Korkalainen Henri , Oksenberg Arie , Leino Akseli , Arnardottir Erna S. , Kulkas Antti , Myllymaa Sami , Töyräs Juha , Leppänen Timo 
Published: February 2020

Current diagnostic parameters estimating obstructive sleep apnoea (OSA) severity have a poor connection to the psychomotor vigilance of OSA patients. Thus, we aimed to investigate how the severity of apnoeas, hypopnoeas and intermittent hypoxaemia is associated with impaired vigilance.We retrospectively examined type I polysomnography data and corresponding psychomotor vigilance tasks (PVTs) of 743 consecutive OSA patients (apnoea–hypopnoea index (AHI) ≥5 events·h−1). Conventional diagnostic parameters (e.g.AHI and oxygen desaturation index (ODI)) and novel parameters (e.g.desaturation severity and obstruction severity) incorporating duration of apnoeas and hypopnoeas as well as depth and duration of desaturations were assessed. Patients were grouped into quartiles based on PVT outcome variables. The odds of belonging to the worst-performing quartile were assessed. Analyses were performed for all PVT outcome variables using binomial logistic regression.A relative 10% increase in median depth of desaturations elevated the odds (ORrange1.20–1.37, p<0.05) of prolonged mean and median reaction times as well as increased lapse count. Similarly, an increase in desaturation severity (ORrange1.26–1.52, p<0.05) associated with prolonged median reaction time. Female sex (ORrange2.21–6.02, p<0.01), Epworth Sleepiness Scale score (ORrange1.05–1.07, p<0.01) and older age (ORrange1.01–1.05, p<0.05) were significant risk factors in all analyses. In contrast, increases in conventional AHI, ODI and arousal index were not associated with deteriorated PVT performance.These results show that our novel parameters describing the severity of intermittent hypoxaemia are significantly associated with increased risk of impaired PVT performance, whereas conventional OSA severity and sleep fragmentation metrics are not. These results underline the importance of developing the assessment of OSA severity beyond the AHI.
Quantitative trait variation in ASD probands and toddler sibling outcomes at 24 months
Authors:   for the IBIS Network, Girault Jessica B. , Swanson Meghan R. , Meera Shoba S. , Grzadzinski Rebecca L. , Shen Mark D. , Burrows Catherine A. , Wolff Jason J. , Pandey Juhi , John Tanya St , Estes Annette , Zwaigenbaum Lonnie , Botteron Kelly N. , Hazlett Heather C. , Dager Stephen R. , Schultz Robert T. , Constantino John N. , Piven Joseph 
Published: February 2020

AbstractBackgroundYounger siblings of children with autism spectrum disorder (ASD) are at increased likelihood of receiving an ASD diagnosis and exhibiting other developmental concerns. It is unknown how quantitative variation in ASD traits and broader developmental domains in older siblings with ASD (probands) may inform outcomes in their younger siblings.MethodsParticipants included 385 pairs of toddler siblings and probands from the Infant Brain Imaging Study. ASD probands (mean age 5.5 years, range 1.7 to 15.5 years) were phenotyped using the Autism Diagnostic Interview-Revised (ADI-R), the Social Communication Questionnaire (SCQ), and the Vineland Adaptive Behavior Scales, Second Edition (VABS-II). Siblings were assessed using the ADI-R, VABS-II, Mullen Scales of Early Learning (MSEL), and Autism Diagnostic Observation Schedule (ADOS) and received a clinical best estimate diagnosis at 24 months using DSM-IV-TR criteria (n = 89 concordant for ASD;n = 296 discordant). We addressed two aims: (1) to determine whether proband characteristics are predictive of recurrence in siblings and (2) to assess associations between proband traits and sibling dimensional outcomes at 24 months.ResultsRegarding recurrence risk, proband SCQ scores were found to significantly predict sibling 24-month diagnostic outcome (OR for a 1-point increase in SCQ = 1.06; 95% CI = 1.01, 1.12). Regarding quantitative trait associations, we found no significant correlations in ASD traits among proband-sibling pairs. However, quantitative variation in proband adaptive behavior, communication, and expressive and receptive language was significantly associated with sibling outcomes in the same domains; proband scores explained 9–18% of the variation in cognition and behavior in siblings with ASD. Receptive language was particularly strongly associated in concordant pairs (ICC = 0.50,p < 0.001).ConclusionsProband ASD symptomology, indexed by the SCQ, is a predictor of familial ASD recurrence risk. While quantitative variation in social communication and restricted and repetitive behavior were not associated among sibling pairs, standardized ratings of proband language and communication explained significant variation in the same domains in the sibling at 24 months, especially among toddlers with an ASD diagnosis. These data suggest that proband characteristics can alert clinicians to areas of developmental concern for young children with familial risk for ASD.
Prediction of neoadjuvant chemotherapeutic efficacy in patients with locally advanced gastric cancer by serum IgG glycomics profiling
Authors: Qin Ruihuan , Yang Yupeng , Chen Hao , Qin Wenjun , Han Jing , Gu Yong , Pan Yiqing , Cheng Xi , Zhao Junjie , Wang Xuefei , Ren Shifang , Sun Yihong , Gu Jianxin 
Published: February 2020

Abstract
Background
Neoadjuvant chemotherapy (NACT) could improve prognosis and survival quality of patients with local advanced gastric cancer (LAGC) by providing an opportunity of radical operation for them. However, no effective method could predict the efficacy of NACT before surgery to avoid the potential toxicity, time-consuming and economic burden of ineffective chemotherapy. Some research has been investigated about the correlation between serum IgG glycosylation and gastric cancer, but the question of whether IgG glycome can reflect the tumor response to NACT is still unanswered.

Method
Serum IgG glycome profiles were analyzed by Ultra Performance Liquid Chromatography in a cohort comprised of 49 LAGC patients of which 25 were categorized as belonging to the NACT response group and 24 patients were assigned to the non-response group. A logistic regression model was constructed to predict the response rate incorporating clinical features and differential N-glycans, while the precision of model was assessed by receiver operating characteristic (ROC) analysis.

Results
IgG N-glycome analysis in pretreatment serum of LAGC patients comprises 24 directly detected glycans and 17 summarized traits. Compared with IgG glycans of non-response group, agalactosylated N-glycans increased while monosialylated N-glycans and digalactosylated N-glycans decreased in the response group. We constructed a model combining patients’ age, histology, chemotherapy regimen, GP4(H3N4F1), GP6(H3N5F1), and GP18(H5N4F1S1), and ROC analysis showed this model has an accurate prediction of NACT response (AUC = 0.840) with the sensitivity of 64.00% and the specificity of 100%.

Conclusion
We here firstly present the profiling of IgG N-glycans in pretreatment serum of LAGC. The alterations in IgG N-glycome may be personalized biomarkers to predict the response to NACT in LAGC and help to illustrate the relationship between immunity and effect of NACT.
Characterization of a New qLTG3–1 Allele for Low-temperature Germinability in Rice from the Wild Species Oryza rufipogon
Authors: Shim Kyu-Chan , Kim Sun Ha , Lee Hyun-Sook , Adeva Cheryl , Jeon Yun-A , Luong Ngoc Ha , Kim Woo-Jin , Akhtamov Mirjalol , Park Yong-Jin , Ahn Sang-Nag 
Published: February 2020

AbstractBackgroundRice (Oryza sativaL.) is generally sensitive to low temperatures, and in production systems that use direct-seeding, low-temperature germinability (LTG) is a desired trait. Previously, the QTLs,qLTG1andqLTG3,that control LTG, were mapped using the BC4F8population, which is a cross of Korean elite cultivar Hwaseong andO. rufipogon(IRGC 105491). We have characterized and analyzed the interaction between the two QTLs, by crossing TR20 that hasO. rufipogonalleles atqLTG1andqLTG3in a Hwaseong background, with Hwaseong, to develop an F2population.ResultsThe F2plants with bothqLTG1andqLTG3alleles fromO. rufipogonshowed higher LTG scores, than the plants with onlyqLTG1orqLTG3. No significant interaction between theqLTG1andqLTG3was observed, indicating that they may regulate LTG via different pathways. Based on its location,qLTG3appears to be allelic withqLTG3–1, a major QTL known to control LTG. To investigate the genetic differences between the two parents, that were controlling LTG, we compared theirqLTG3–1sequences. In the coding region, three sequence variations leading to amino acid changes were identified between the Hwaseong andO. rufipogon. Of these, a non-synonymous substitution at the 62nd amino acid site, had not previously been reported. To understand the cause of the LTG variations between the parents, we genotyped three sequence variations ofqLTG3–1, that were identified in 98 Asian cultivated rice accessions (Oryza sativaL.). The 98 accessions were classified into 5 haplotypes, based on three variations and a 71-bp deletion. Mean low-temperature germination rates were compared among the haplotypes, and haplotype 5 (O. rufipogon-type) showed a significantly higher germination rate than haplotype 2 (Nipponbare-type), and haplotype 3 (Italica Livorno-type).ConclusionsTheO. rufipogon qLTG3–1allele can be utilized for the improvement of LTG in rice breeding programs. Nearly isogenic lines harboring bothqLTG1andqLTG3–1alleles fromO. rufipogon,showed higher LTG scores than the NILs withqLTG1orqLTG3–1alone, and the two QTLs regulate LTG via different pathways. To our knowledge, this is the first report to detect a newqLTG3–1allele and analyze the interaction of the two LTG QTLs in a nearly isogenic background.
Primary orthologs from local sequence context
Authors: Gao Kun , Miller Jonathan 
Published: February 2020

AbstractBackgroundThe evolutionary history of genes serves as a cornerstone of contemporary biology. Most conserved sequences in mammalian genomes don’t code for proteins, yielding a need to infer evolutionary history of sequences irrespective of what kind of functional element they may encode. Thus, sequence-, as opposed to gene-, centric modes of inferring paths of sequence evolution are increasingly relevant. Customarily, homologous sequences derived from the same direct ancestor, whose ancestral position in two genomes is usually conserved, are termed “primary” (or “positional”) orthologs. Methods based solely on similarity don’t reliably distinguish primary orthologs from other homologs; for this, genomic context is often essential. Context-dependent identification of orthologs traditionally relies on genomic context over length scales characteristic of conserved gene order or whole-genome sequence alignment, and can be computationally intensive.ResultsWe demonstrate that short-range sequence context—as short as a single “maximal” match— distinguishes primary orthologs from other homologs across whole genomes. On mammalian whole genomes not preprocessed by repeat-masker, potential orthologs are extracted by genome intersection as “non-nested maximal matches:” maximal matches that are not nested into other maximal matches. It emerges that on both nucleotide and gene scales, non-nested maximal matches recapitulate primary or positional orthologs with high precision and high recall, while the corresponding computation consumes less than one thirtieth of the computation time required by commonly applied whole-genome alignment methods. In regions of genomes that would be masked by repeat-masker, non-nested maximal matches recover orthologs that are inaccessible to Lastz net alignment, for which repeat-masking is a prerequisite. mmRBHs, reciprocal best hits of genes containing non-nested maximal matches, yield novel putative orthologs, e.g. around 1000 pairs of genes for human-chimpanzee.ConclusionsWe describe an intersection-based method that requires neither repeat-masking nor alignment to infer evolutionary history of sequences based on short-range genomic sequence context. Ortholog identification based on non-nested maximal matches is parameter-free, and less computationally intensive than many alignment-based methods. It is especially suitable for genome-wide identification of orthologs, and may be applicable to unassembled genomes. We are agnostic as to the reasons for its effectiveness, which may reflect local variation of mean mutation rate.
Dynamics of mobile genetic elements of Listeria monocytogenes persisting in ready-to-eat seafood processing plants in France
Authors: Palma Federica , Brauge Thomas , Radomski Nicolas , Mallet Ludovic , Felten Arnaud , Mistou Michel-Yves , Brisabois Anne , Guillier Laurent , Midelet-Bourdin Graziella 
Published: February 2020

AbstractBackgroundListeria monocytogenesClonal Complexes (CCs) have been epidemiologically associated with foods, especially ready-to-eat (RTE) products for which the most likely source of contamination depends on the occurrence of persisting clones in food-processing environments (FPEs). As the ability ofL. monocytogenesto adapt to environmental stressors met in the food chain challenges the efforts to its eradication from FPEs, the threat of persistent strains to the food industry and public health authorities continues to rise. In this study, 94 food and FPEsL. monocytogenesisolates, representing persistent subtypes contaminating three French seafood facilities over 2–6 years, were whole-genome sequenced to characterize their genetic diversity and determine the biomarkers associated with long-term survival in FPEs.ResultsFood and FPEs isolates belonged to five CCs, comprising long-term intra- and inter-plant persisting clones. Mobile genetic elements (MGEs) such as plasmids, prophages and transposons were highly conserved within CCs, some of which harboured genes for resistance to chemical compounds and biocides used in the processing plants. Some of these genes were found in a 90.8 kbp plasmid, predicted to be” mobilizable”, identical in isolates from CC204 and CC155, and highly similar to an 81.6 kbp plasmid from isolates belonging to CC7. These similarities suggest horizontal transfer between isolates, accompanied by deletion and homologous recombination in isolates from CC7. Prophage profiles characterized persistent clonal strains and several prophage-loci were plant-associated. Notably, a persistent clone from CC101 harboured a novel 31.5 kbp genomic island that we namedListeriagenomic island 3 (LGI3), composed by plant-associated loci and chromosomally integrating cadmium-resistance determinantscadA1C.ConclusionsGenome-wide analysis indicated that inter- and intra-plant persisting clones harbour conserved MGEs, likely acquired in FPEs and maintained by selective pressures. The presence of closely related plasmids inL. monocytogenesCCs supports the hypothesis of horizontal gene transfer conferring enhanced survival to FPE-associated stressors, especially in hard-to-clean harbourage sites. Investigating the MGEs evolutionary and transmission dynamics provides additional resolution to trace-back potentially persistent clones. The biomarkers herein discovered provide new tools for better designing effective strategies for the removal or reduction of residentL. monocytogenesin FPEs to prevent contamination of RTE seafood.
Comparison of morphometry and ventricular function of healthy and smoking young people
Authors: Batista Ana Natália Ribeiro , Garcia Thais , Franco Estefânia Aparecida Thomé , Azevedo Paula Schmidt , Barbosa Mauricio Fregonesi , Zornoff Leonardo Antonio Mamede , Minicucci Marcos Ferreira , de Paiva Sergio Alberto Rupp , Zucchi José William , de Godoy Irma , Tanni Suzana Erico 
Published: February 2020

Abstract
Background
Tobacco smoke is one of the most significant risk factors for cardiovascular diseases and damages in the myocardial tissue directly. Cardiac magnetic resonance (CMR) has been used and is a promising tool to evaluate morphometry and cardiac function in humans. The objective of this study was to evaluate associations of smoking with morphometry and cardiac function by CMR technique in young adult smokers.

Methods
Altogether, 49 volunteers (22 smokers and 27 non-smokers) were included in the study. The comparisons between groups were performed by multiple linear regression adjusting for body mass index and gender.

Results
In the morphometric and functional evaluation of the left ventricle, we observed statistical significant lower values of end-diastolic volume (EDV) (p = 0.02), ejection volume (EV) (p = 0.001) and indexed ejection volume (IEV) (p = 0.007) in smokers when compared to no-smoker group. Right ventricle showed statistical significant lower values of EDV (p = < 0.001), end-systolic volume (p = 0.01), EV (p = < 0.001), IEV (p = 0.001), indexed end-diastolic volume (p = 0.001) and major axis (p = 0.01) in smokers when compared to non-smokers group.

Conclusions
There is a strongly association of smoking in young adult and cardiac function decline, even adjusted by cofounders, which compromises the proper functioning of the heart. Evidence confirms that smoking can directly influence the cardiac function, even without atherosclerosis or other chronic comorbidities, associated with increased risk of cardiovascular diseases.
Association between perceived environmental pollution and health among urban and rural residents-a Chinese national study
Authors: Yang Ting 
Published: February 2020

Abstract
Background
China’s economic boom has led to severe environmental pollution, which has created significant health risks for residents. Although current studies have found urban residents can sense the harmful effects of environmental pollution in China, few studies have talked about their rural counterparts’ attitudes towards the health impacts of environmental pollution. Similarly, little research has talked about the inequality of environmental awareness between urban and rural residents.

Methods
Descriptive and analytical statistics were used for the data analyses based on a national survey, namely, The 3rd Survey on the Status of Chinese Women in 2010, which was jointly conducted by the All China Women’s Federation and the China Statistical Bureau in 2010. A total of 24741observations were selected.

Results
Among urban residents, 67.21% reported that their total health was good, which was 1.35% lower than the reported rate of their rural counterparts; 25.88% of urban residents reported that their total health was general, which was nearly 3% higher than the reported rate of their rural counterparts; 6.91% of urban residents reported that their total health was poor, which was 1.63% lower than the reported rate of their rural counterparts. The study also found that the rates of urban residents who perceived air pollution (35.67%), water pollution (17.96%), garbage pollution (25.05%), and noise pollution (32.05%) were higher than those of their rural counterparts. Perceived air pollution, and perceived noise pollution both had a negative effect on urban residents’ good health (B = − 0.14, p < 0.05; B = -0.23, p < 0.001). Perceived garbage pollution had a positive effect on urban residents’ poor health (B = 0.33, p < 0.01). Perceived water pollution had no significant effect on urban residents’ health. The four types of perceived environmental pollution all had insignificant effects on rural residents’ health.

Conclusions
Rural residents lack awareness of the impacts of environmental pollution on health, which may create risks and vulnerability within the rural environment and the livelihood of these residents. Great attention should be paid to the impacts of environmental pollution on the health of not only urban residents but also rural residents, which will highly improve the support of green development among the public in China.