bluuebunny/crossref_metadata_2025_split huggingface dataset:
Alterations of 5-hydroxymethylation in circulating cell-free DNA reflect molecular distinctions of subtypes of non-Hodgkin lymphoma
Authors: Chiu Brian C.-H. , Chen Chang , You Qiancheng , Chiu Rudyard , Venkataraman Girish , Zeng Chang , Zhang Zhou , Cui Xiaolong , Smith Sonali M. , He Chuan , Zhang Wei 
Published: February 2021

AbstractThe 5-methylcytosines (5mC) have been implicated in the pathogenesis of diffuse large B-cell lymphoma (DLBCL) and follicular lymphoma (FL). However, the role of 5-hydroxymethylcytosines (5hmC) that are generated from 5mC through active demethylation, in lymphomagenesis is unknown. We profiled genome-wide 5hmC in circulating cell-free DNA (cfDNA) from 73 newly diagnosed patients with DLBCL and FL. We identified 294 differentially modified genes between DLBCL and FL. The differential 5hmC in the DLBCL/FL-differentiating genes co-localized with enhancer marks H3K4me1 and H3K27ac. A four-gene panel (CNN2, HMG20B, ACRBP, IZUMO1) robustly represented the overall 5hmC modification pattern that distinguished FL from DLBCL with an area under curve of 88.5% in the testing set. The median 5hmC modification levels in signature genes showed potential for separating patients for risk of all-cause mortality. This study provides evidence that genome-wide 5hmC profiles in cfDNA differ between DLBCL and FL and could be exploited as a non-invasive approach.
Differences in MTHFR and LRRK2 variant’s association with sporadic Parkinson’s disease in Mexican Mestizos correlated to Native American ancestry
Authors: Romero-Gutiérrez Elizabeth , Vázquez-Cárdenas Paola , Moreno-Macías Hortensia , Salas-Pacheco José , Tusié-Luna Teresa , Arias-Carrión Oscar 
Published: February 2021

AbstractParkinson’s disease (PD), a common neurodegenerative disorder, has a complex etiology where environmental and genetic factors intervene. While a number of genes and variants have been identified in recent decades as causative or protective agents of this condition, a limited number of studies have been conducted in mixed populations, such as Mexican Mestizos. The historical convergence of two founding groups and three ethnicities, and the increasing north-to-south gradient of Native American ancestry in Mexico resulted in a subpopulation structure with considerable genetic diversity. In this work, we investigate the influence of 21 known susceptibility variants for PD. Our case–control study, with a cohort of 311 Mexican Mestizo subjects, found a significant risk association for the variant rs1491942 inLRRK2. However, when stratification by ancestry was performed, a risk effect forMTHFRrs1801133 was observed only in the group with the highest percentage of European ancestry, and the PD risk effect forLRRK2rs1491942 was significant in subjects with a higher ratio of Native American ancestry. Meta-analyses of these SNP revealed the effect ofLRRK2rs1491942 to be even more significant than previously described in populations of European descent. Although corroboration is necessary, our findings suggest that polymorphism rs1491942 may be useful as a risk marker of PD in Mexican Mestizos with greater Native American ancestry. The absence of associations with the remaining known risk factors is, in itself, a relevant finding and invites further research into the shared risk factors’ role in the pathophysiological mechanisms of this neurodegenerative disorder.
Specialist respiratory outreach: a case-finding initiative for identifying undiagnosed COPD in primary care
Authors: Ray Emma , Culliford David , Kruk Helen , Gillett Kate , North Mal , Astles Carla M. , Hicks Alexander , Johnson Matthew , Lin Sharon Xiaowen , Orlando Rosanna , Thomas Mike , Jordan Rachel E. , Price David , Konstantin Mita , Wilkinson Tom M. A. 
Published: February 2021

AbstractCOPD remains largely undiagnosed or is diagnosed late in the course of disease. We report findings of a specialist outreach programme to identify undiagnosed COPD in primary care. An electronic case-finding algorithm identified 1602 at-risk patients from 12 practices who were invited to attend the clinic. Three hundred and eighty-three (23.9%) responded and 288 were enrolled into the study. Forty-eight (16.6%) had undiagnosed mild and 28 (9.7%) had moderate airway obstruction, meeting spirometric diagnostic criteria for COPD. However, at 12 months only 8 suspected COPD patients (10.6%) had received a diagnostic label in their primary care record. This constituted 0.38% of the total patient population, as compared with 0.31% of control practices, p = 0.306. However, if all patients with airway obstruction received a coding of COPD, then the diagnosis rate in the intervention group would have risen by 0.84%. Despite the low take-up and diagnostic yield, this programme suggests that integrated case-finding strategies could improve COPD recognition.
Electrochemical metrics for corrosion resistant alloys
Authors: Nyby Clara , Guo Xiaolei , Saal James E. , Chien Szu-Chia , Gerard Angela Y. , Ke Huibin , Li Tianshu , Lu Pin , Oberdorfer Christian , Sahu Sarita , Li Sirui , Taylor Christopher D. , Windl Wolfgang , Scully John R. , Frankel Gerald S. 
Published: February 2021

AbstractCorrosion is an electrochemical phenomenon. It can occur via different modes of attack, each having its own mechanisms, and therefore there are multiple metrics for evaluating corrosion resistance. In corrosion resistant alloys (CRAs), the rate of localized corrosion can exceed that of uniform corrosion by orders of magnitude. Therefore, instead of uniform corrosion rate, more complex electrochemical parameters are required to capture the salient features of corrosion phenomena. Here, we collect a database with an emphasis on metrics related to localized corrosion. The six sections of the database include data on various metal alloys with measurements of (1) pitting potential, Epit, (2) repassivation potential, Erp, (3) crevice corrosion potential, Ecrev, (4) pitting temperature, Tpit, (5) crevice corrosion temperature, Tcrev, and (6) corrosion potential, Ecorr, corrosion current density, icorr, passivation current density, ipass, and corrosion rate. The experimental data were collected from 85 publications and include Al- and Fe-based alloys, high entropy alloys (HEAs), and a Ni-Cr-Mo ternary system. This dataset could be used in the design of highly corrosion resistant alloys.
Chromosome-scale genome assembly of the sea louse Caligus rogercresseyi by SMRT sequencing and Hi-C analysis
Authors: Gallardo-Escárate Cristian , Valenzuela-Muñoz Valentina , Nuñez-Acuña Gustavo , Valenzuela-Miranda Diego , Gonçalves Ana Teresa , Escobar-Sepulveda Hugo , Liachko Ivan , Nelson Bradley , Roberts Steven , Warren Wesley 
Published: February 2021

AbstractCaligus rogercresseyi, commonly known as sea louse, is an ectoparasite copepod that impacts the salmon aquaculture in Chile, causing losses of hundreds of million dollars per year. In this study, we report a chromosome-scale assembly of the sea louse (C. rogercresseyi) genome based on single-molecule real-time sequencing (SMRT) and proximity ligation (Hi-C) analysis. Coding RNAs and non-coding RNAs, and specifically long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) were identified through whole transcriptome sequencing from different life stages. A total of 23,686 protein-coding genes and 12,558 non-coding RNAs were annotated. In addition, 6,308 lncRNAs and 5,774 miRNAs were found to be transcriptionally active from larvae to adult stages. Taken together, this genomic resource for C. rogercresseyi represents a valuable tool to develop sustainable control strategies in the salmon aquaculture industry.
Gene expression and epigenetics reveal species-specific mechanisms acting upon common molecular pathways in the evolution of task division in bees
Authors: Araujo Natalia de Souza , Arias Maria Cristina 
Published: February 2021

AbstractA striking feature of advanced insect societies is the existence of workers that forgo reproduction. Two broad types of workers exist in eusocial bees: nurses who care for their young siblings and the queen, and foragers who guard the nest and forage for food. Comparisons between these two worker subcastes have been performed in honeybees, but data from other bees are scarce. To understand whether similar molecular mechanisms are involved in nurse-forager differences across distinct species, we compared gene expression and DNA methylation profiles between nurses and foragers of the buff-tailed bumblebee Bombus terrestris and the stingless bee Tetragonisca angustula. These datasets were then compared to previous findings from honeybees. Our analyses revealed that although the expression pattern of genes is often species-specific, many of the biological processes and molecular pathways involved are common. Moreover, the correlation between gene expression and DNA methylation was dependent on the nucleotide context, and non-CG methylation appeared to be a relevant factor in the behavioral changes of the workers. In summary, task specialization in worker bees is characterized by a plastic and mosaic molecular pattern, with species-specific mechanisms acting upon broad common pathways across species.
Comparative study on heat transfer and friction drag in the flow of various hybrid nanofluids effected by aligned magnetic field and nonlinear radiation
Authors: Khan M. Riaz , Li Mingxia , Mao Shipeng , Ali Rashid , Khan Suliman 
Published: February 2021

AbstractThe key purpose of the existing article is to discuss the effects of various hybrid nanofluids and a simple nanofluid over the heat transfer and friction drags along a stretched surface. The various kinds of hybrid nanofluids and a simple nanofluid together with the effects of aligned magnetic field, nonlinear radiation and suction have been taken into consideration. These hybrid nanofluids are prepared by suspending a couple of distinct nanoparticles $$Cu$$

Cu

and $$A{l}_{2}{O}_{3}$$

A

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2

O
3

into the base fluids $${H}_{2}O$$

H
2

O

and $${C}_{2}{H}_{6}{O}_{2}$$

C
2

H
6

O
2

. The comparison of various graphical results of skin friction coefficient, rate of heat transfer, velocity and temperature for two different hybrid nanofluids $$Cu{-}A{l}_{2}{O}_{3}$$

C
u
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A

l
2

O
3

/$${H}_{2}O$$

H
2

O

, $$Cu{-}A{l}_{2}{O}_{3}$$

C
u
-
A

l
2

O
3

/$${H}_{2}O{-}{C}_{2}{H}_{6}{O}_{2}$$

H
2

O
-

C
2

H
6

O
2

and a simple nanofluid $$A{l}_{2}{O}_{3}$$

A

l
2

O
3

/$${H}_{2}O$$

H
2

O

is considered. Moreover, the impact of surface stretching, aligned magnetic field and thermal radiation over the velocity, temperature, skin friction coefficient and local Nusselt number are also considered. The outcomes drawn from this modern research is that the hybrid nanofluid $$Cu{-}A{l}_{2}{O}_{3}$$

C
u
-
A

l
2

O
3

/$${H}_{2}O{-}{C}_{2}{H}_{6}{O}_{2}$$

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2

O
-

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2

H
6

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2

is quite effective in cooling and heating in comparison to the other hybrid nanofluids $$Cu{-}A{l}_{2}{O}_{3}$$

C
u
-
A

l
2

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3

/$${H}_{2}O$$

H
2

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, $$Cu{-}A{l}_{2}{O}_{3}$$

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-
A

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2

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3

/$${C}_{2}{H}_{6}{O}_{2}$$

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2

H
6

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2

and a simple nanofluid $$A{l}_{2}{O}_{3}/{H}_{2}O$$

A

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2

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3

/

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2

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. Based on these findings we could say that the suspension of multiple particles in the composition of two or more base fluids provides a better rate of heat transfer and limits the friction drag.
Non-collinear Hox gene expression in bivalves and the evolution of morphological novelties in mollusks
Authors: Salamanca-Díaz David A. , Calcino Andrew D. , de Oliveira André L. , Wanninger Andreas 
Published: February 2021

AbstractHox genes are key developmental regulators that are involved in establishing morphological features during animal ontogeny. They are commonly expressed along the anterior–posterior axis in a staggered, or collinear, fashion. In mollusks, the repertoire of body plans is widely diverse and current data suggest their involvement during development of landmark morphological traits in Conchifera, one of the two major lineages that comprises those taxa that originated from a uni-shelled ancestor (Monoplacophora, Gastropoda, Cephalopoda, Scaphopoda, Bivalvia). For most clades, and bivalves in particular, data on Hox gene expression throughout ontogeny are scarce. We thus investigated Hox expression during development of the quagga mussel, Dreissena rostriformis, to elucidate to which degree they might contribute to specific phenotypic traits as in other conchiferans. The Hox/ParaHox complement of Mollusca typically comprises 14 genes, 13 of which are present in bivalve genomes including Dreissena. We describe here expression of 9 Hox genes and the ParaHox gene Xlox during Dreissena development. Hox expression in Dreissena is first detected in the gastrula stage with widely overlapping expression domains of most genes. In the trochophore stage, Hox gene expression shifts towards more compact, largely mesodermal domains. Only few of these domains can be assigned to specific developing morphological structures such as Hox1 in the shell field and Xlox in the hindgut. We did not find traces of spatial or temporal staggered expression of Hox genes in Dreissena. Our data support the notion that Hox gene expression has been coopted independently, and to varying degrees, into lineage-specific structures in the respective conchiferan clades. The non-collinear mode of Hox expression in Dreissena might be a result of the low degree of body plan regionalization along the bivalve anterior–posterior axis as exemplified by the lack of key morphological traits such as a distinct head, cephalic tentacles, radula apparatus, and a simplified central nervous system.
A randomized controlled trial investigating the impact of maternal dietary supplementation with pomegranate juice on brain injury in infants with IUGR
Authors: Ross Madeline M. , Cherkerzian Sara , Mikulis Nicole D. , Turner Daria , Robinson Julian , Inder Terrie E. , Matthews Lillian G. 
Published: February 2021

AbstractAnimal studies have demonstrated the therapeutic potential of polyphenol-rich pomegranate juice. We recently reported altered white matter microstructure and functional connectivity in the infant brain following in utero pomegranate juice exposure in pregnancies with intrauterine growth restriction (IUGR). This double-blind exploratory randomized controlled trial further investigates the impact of maternal pomegranate juice intake on brain structure and injury in a second cohort of IUGR pregnancies diagnosed at 24–34 weeks’ gestation. Ninety-nine mothers and their eligible fetuses (n = 103) were recruited from Brigham and Women’s Hospital and randomly assigned to 8 oz pomegranate (n = 56) or placebo (n = 47) juice to be consumed daily from enrollment to delivery. A subset of participants underwent fetal echocardiogram after 2 weeks on juice with no evidence of ductal constriction. 57 infants (n = 26 pomegranate,n = 31 placebo) underwent term-equivalent MRI for assessment of brain injury, volumes and white matter diffusion. No significant group differences were found in brain volumes or white matter microstructure; however, infants whose mothers consumed pomegranate juice demonstrated lower risk for brain injury, including any white or cortical grey matter injury compared to placebo. These preliminary findings suggest pomegranate juice may be a safe in utero neuroprotectant in pregnancies with known IUGR warranting continued investigation.Clinical trial registration: NCT04394910,https://clinicaltrials.gov/ct2/show/NCT04394910, Registered May 20, 2020, initial participant enrollment January 16, 2016.
IgG acquisition against PfEMP1 PF11_0521 domain cassette DC13, DBLβ3_D4 domain, and peptides located within these constructs in children with cerebral malaria
Authors: Badaut Cyril , Visitdesotrakul Pimnitah , Chabry Aurélie , Bigey Pascal , Tornyigah Bernard , Roman Jocelyne , Maroufou Jules Alao , Amoussou Annick , Ayivi Blaise Serge , Sagbo Gratien , Ndam Nicaise Tuikue , Oleinikov Andrew V. , Tahar Rachida 
Published: February 2021

AbstractThe Plasmodium falciparum erythrocyte-membrane-protein-1 (PF3D7_1150400/PF11_0521) contains both domain cassette DC13 and DBLβ3 domain binding to EPCR and ICAM-1 receptors, respectively. This type of PfEMP1 proteins with dual binding specificity mediate specific interactions with brain micro-vessels endothelium leading to the development of cerebral malaria (CM). Using plasma collected from children at time of hospital admission and after 30 days, we study an acquisition of IgG response to PF3D7_1150400/PF11_0521 DC13 and DBLβ3_D4 recombinant constructs, and five peptides located within these constructs, specifically in DBLα1.7_D2 and DBLβ3_D4 domains. We found significant IgG responses against the entire DC13, PF11_0521_DBLβ3_D4 domain, and peptides. The responses varied against different peptides and depended on the clinical status of children. The response was stronger at day 30, and mostly did not differ between CM and uncomplicated malaria (UM) groups. Specifically, the DBLβ3 B3-34 peptide that contains essential residues involved in the interaction between PF11_0521 DBLβ3_D4 domain and ICAM-1 receptor demonstrated significant increase in reactivity to IgG1 and IgG3 antibodies at convalescence. Further, IgG reactivity in CM group at time of admission against functionally active (ICAM-1-binding) PF11_0521 DBLβ3_D4 domain was associated with protection against severe anemia. These results support development of vaccine based on the PF3D7_1150400/PF11_0521 structures to prevent CM.
A self-referenced in-situ arrival time monitor for X-ray free-electron lasers
Authors: Diez Michael , Galler Andreas , Schulz Sebastian , Boemer Christina , Coffee Ryan N. , Hartmann Nick , Heider Rupert , Wagner Martin S. , Helml Wolfram , Katayama Tetsuo , Sato Tokushi , Sato Takahiro , Yabashi Makina , Bressler Christian 
Published: February 2021

AbstractWe present a novel, highly versatile, and self-referenced arrival time monitor for measuring the femtosecond time delay between a hard X-ray pulse from a free-electron laser and an optical laser pulse, measured directly on the same sample used for pump-probe experiments. Two chirped and picosecond long optical supercontinuum pulses traverse the sample with a mutually fixed time delay of 970 fs, while a femtosecond X-ray pulse arrives at an instant in between both pulses. Behind the sample the supercontinuum pulses are temporally overlapped to yield near-perfect destructive interference in the absence of the X-ray pulse. Stimulation of the sample with an X-ray pulse delivers non-zero contributions at certain optical wavelengths, which serve as a measure of the relative arrival time of the X-ray pulse with an accuracy of better than 25 fs. We find an excellent agreement of our monitor with the existing timing diagnostics at the SACLA XFEL with a Pearson correlation value of 0.98. We demonstrate a high sensitivity to measure X-ray pulses with pulse energies as low as 30 $$\upmu $$
μ
J. Using a free-flowing liquid jet as interaction sample ensures the full replacement of the sample volume for each X-ray/optical event, thus enabling its utility even at MHz repetition rate XFEL sources.
Interevent-time distribution and aftershock frequency in non-stationary induced seismicity
Authors: Post Richard A. J. , Michels Matthias A. J. , Ampuero Jean-Paul , Candela Thibault , Fokker Peter A. , van Wees Jan-Diederik , Hofstad Remco W. van der , Heuvel Edwin R. van den 
Published: February 2021

AbstractThe initial footprint of an earthquake can be extended considerably by triggering of clustered aftershocks. Such earthquake–earthquake interactions have been studied extensively for data-rich, stationary natural seismicity. Induced seismicity, however, is intrinsically inhomogeneous in time and space and may have a limited catalog of events; this may hamper the distinction between human-induced background events and triggered aftershocks. Here we introduce a novel Gamma Accelerated-Failure-Time model for efficiently analyzing interevent-time distributions in such cases. It addresses the spatiotemporal variation and quantifies, per event, the probability of each event to have been triggered. Distentangling the obscuring aftershocks from the background events is a crucial step to better understand the causal relationship between operational parameters and non-stationary induced seismicity. Applied to the Groningen gas field in the North of the Netherlands, our model elucidates geological and operational drivers of seismicity and has been used to test for aftershock triggering. We find that the hazard rate in Groningen is indeed enhanced after each event and conclude that aftershock triggering cannot be ignored. In particular we find that the non-stationary interevent-time distribution is well described by our Gamma model. This model suggests that 27.0(± 8.5)% of the recorded events in the Groningen field can be attributed to triggering.
Copper-67 radioimmunotheranostics for simultaneous immunotherapy and immuno-SPECT
Authors: Hao Guiyang , Mastren Tara , Silvers William , Hassan Gedaa , Öz Orhan K. , Sun Xiankai 
Published: February 2021

AbstractCopper-67 (t1/2 = 2.58 days) decays by β− ($$\text{E}_{{\upbeta^{-}\text{max}}}$$

E

β
-

max

: 562 keV) and γ-rays (93 keV and 185 keV) rendering it with potential for both radionuclide therapy and single-photon emission computed tomography (SPECT) imaging. Prompted by the recent breakthrough of 67Cu production with high specific activity, high radionuclidic purity, and sufficient quantities, the interest in the theranostic potential of 67Cu has been rekindled. This work addresses the practicability of developing 67Cu-labeled antibodies with substantially improved quality for cancer radioimmunotheranostics. Proof of concept is demonstrated with pertuzumab, a US-FDA-approved monoclonal antibody for combination therapies of HER2-positive breast cancer. With an average number of 1.9 chelators coupled to each antibody, we achieved a two-order of magnitude increase in radiolabeling efficiency compared to literature reports. In a preclinical therapeutic study, mice (n = 4–7/group) bearing HER2+ xenografts exhibited a 67Cu-dose dependent tumor-growth inhibition from 67Cu-labeled-Pertuzumab co-administered with trastuzumab. Furthermore, greater tumor size reduction was observed with 67Cu-labeled-pertuzumab formulations of higher specific activity. The potential of SPECT imaging with 67Cu radiopharmaceuticals was tested after 67Cu-labeled-Pertuzumab administration. Impressively, all tumors were clearly visualized by SPECT imaging with 67Cu-labeled-Pertuzumab even at day 5 post injection. This work demonstrates it is practical to use 67Cu radioimmunoconjugates for cancer radioimmunotheranostics.