bluuebunny/crossref_metadata_2025_split huggingface dataset:
Probing the waveguiding properties of quasi-2D organic semiconductor through optical imaging
Authors: Zhong Zhen , Gong Xiuduan , Lin Shenghuang , Yuan Jian 
Published: June 2021

Abstract
Though there have been many investigations focusing on organic semiconductors, how to fully probe their waveguiding properties is still rarely reported. In this work, the light propagation loss in the Znq2 samples was detected by a modified light transmission path. The results showed that the optical propagation loss coefficient of Znq2 nanorods is ∼0.16 dB μm−1. Our work fully reveals the waveguiding properties in 2D organic semiconductor by 2D & 3D imaging, which may offer a new reference for exploring novel optical properties of 2D organic semiconductors.
Second phase structure analysis and wear behavior of the ultra-high manganese steel
Authors: Wang Zhenghui , Xie Jingpei , Li Qian , Wang Wenyan , Wang Aiqin , Liu Pei 
Published: June 2021

Abstract
The high manganese steel is widely used in wear-resisting parts of the cone crusher, such as the grinding mill wall and crushing wall. In this work, the microstructure and wear resistance of an ultra-high manganese steel (Mn18Cr2Mo) were analyzed by electron diffraction and high-resolution transmission electron microscope (HRTEM) observation and impact abrasive wear test. The results show that there are spherical or block Mo2C and strip-like (Fe, Cr)3C phases in Mn18Cr2Mo manganese steel. The orientation of the Mo2C phase and the austenite matrix are [001]austenite//

10

1

¯

Mo2C, (020)austenite//(020)Mo2C,

2

¯

00

austenite//(202)Mo2C and

2

¯

20

austenite//(242)Mo2C. The that of the (Fe, Cr)3C phase and the austenite matrix are [011]austenite//

12

1

¯

(Fe, Cr)3C and

11

1

¯

austenite//(210)(Fe, Cr)3C. Besides,

1

¯

1

1

¯

austenite is approximately parallel to

1

1

¯

3

(Fe, Cr)3C. The interface relation of (002)austenite is approximately parallel to

1

¯

2

¯

3

(Fe, Cr)3C. Owing to high density dislocations, deformation bands, microcrystal and non-crystalline, the wear resistance of the Mn18Cr2Mo manganese steel is 1.83 times that of the Mn13 manganese steel under the impact abrasive wear test.
Time between diagnosis and achievement of virologic suppression in people living with HIV
Authors: Ilagan Danica Joy C , Eitniear Lindsey , Cole Kelli , Duggan Joan , Sahloff Eric 
Published: June 2021

Abstract

Purpose
Data support the individual and public health advantages of shortened time intervals between HIV diagnosis, initiation of antiretroviral therapy (ART), and virologic suppression. The time from HIV diagnosis to linkage to care, initiation of ART, and virologic suppression was evaluated in newly diagnosed, ART-naive individuals after structured programmatic changes were implemented to reduce time to virologic suppression (TVS).

Methods
The retrospective cohort included newly diagnosed, ART-naive adult patients receiving care in a Midwestern Ryan White Clinic. Study periods were between January 1, 2015, and December 31, 2015 (delayed treatment group) and January 1, 2017, and December 31, 2017 (rapid treatment group). Changes during the intervention time period were related to access to care and ART. The primary outcome of time from HIV diagnosis to virologic suppression was compared between the groups. Secondary outcomes included the time from diagnosis to linkage to care and the time to initiation of ART.

Results
Twenty-four and 35 individuals were included in the control and intervention groups, respectively. Median (interquartile range) time from diagnosis to viral suppression was 137 (77-318) days in the delayed treatment group vs 76.5 (51-151) days in the rapid treatment group (P = 0.021). Time from diagnosis to first clinic visit remained similar (median of 13.5 vs 15 days, P = 0.859), while time from first clinic visit to initiation of ART decreased significantly (median of 15 vs 0 days, P &lt; 0.001).

Conclusion
Time from first clinic visit to ART initiation was significantly shortened in this intervention and was the driving force to decreasing TVS. Additional research into barriers impacting time from diagnosis to linkage to care are needed to further shorten TVS.
Synthesizing Indirect Effects in Mediation Models With Meta-Analytic Methods
Authors: Cheung Mike W-L 
Published: June 2021

AbstractAimsA mediator is a variable that explains the underlying mechanism between an independent variable and a dependent variable. The indirect effect indicates the effect from the predictor to the outcome variable via the mediator. In contrast, the direct effect represents the predictor's effort on the outcome variable after controlling for the mediator.MethodsA single study rarely provides enough evidence to answer research questions in a particular domain. Replications are generally recommended as the gold standard to conduct scientific research. When a sufficient number of studies have been conducted addressing similar research questions, a meta-analysis can be used to synthesize those studies' findings.ResultsThe main objective of this paper is to introduce two frameworks to integrating studies using mediation analysis. The first framework involves calculating standardized indirect effects and direct effects and conducting a multivariate meta-analysis on those effect sizes. The second one uses meta-analytic structural equation modeling to synthesize correlation matrices and fit mediation models on the average correlation matrix. We illustrate these procedures on a real dataset using the R statistical platform.ConclusionThis paper closes with some further directions for future studies.
BioVLAB-Cancer-Pharmacogenomics: tumor heterogeneity and pharmacogenomics analysis of multi-omics data from tumor on the cloud
Authors: Park Sungjoon , Lee Dohoon , Kim Youngkuk , Lim Sangsoo , Chae Heejoon , Kim Sun 
Published: June 2021

Abstract

Motivation
Multi-omics data in molecular biology has accumulated rapidly over the years. Such data contains valuable information for research in medicine and drug discovery. Unfortunately, data-driven research in medicine and drug discovery is challenging for a majority of small research labs due to the large volume of data and the complexity of analysis pipeline.

Results
We present BioVLAB-Cancer-Pharmacogenomics, a bioinformatics system that facilitates analysis of multi-omics data from breast cancer to analyze and investigate intratumor heterogeneity and pharmacogenomics on Amazon Web Services. Our system takes multi-omics data as input to perform tumor heterogeneity analysis in terms of TCGA data and deconvolve-and-match the tumor gene expression to cell line data in CCLE using DNA methylation profiles. We believe that our system can help small research labs perform analysis of tumor multi-omics without worrying about computational infrastructure and maintenance of databases and tools.

Availability and implementation
http://biohealth.snu.ac.kr/software/biovlab_cancer_pharmacogenomics.

Supplementary information
Supplementary data are available at Bioinformatics online.
Pain, No Gain: Acute Pain Interrupts Motor Imagery Processes and Affects Mental Training-Induced Plasticity
Authors: Neige Cécilia , Lebon Florent , Mercier Catherine , Gaveau Jérémie , Papaxanthis Charalambos , Ruffino Célia 
Published: June 2021

Abstract
Pain influences both motor behavior and neuroplastic adaptations induced by physical training. Motor imagery (MI) is a promising method to recover motor functions, for instance in clinical populations with limited endurance or concomitant pain. However, the influence of pain on the MI processes is not well established. This study investigated whether acute experimental pain could modulate corticospinal excitability assessed at rest and during MI (Exp. 1) and limit the use-dependent plasticity induced by MI practice (Exp. 2). Participants imagined thumb movements without pain or with painful electrical stimulations applied either on digit V or over the knee. We used transcranial magnetic stimulation to measure corticospinal excitability at rest and during MI (Exp. 1) and to evoke involuntary thumb movements before and after MI practice (Exp. 2). Regardless of its location, pain prevented the increase of corticospinal excitability that is classically observed during MI. In addition, pain blocked use-dependent plasticity following MI practice, as testified by a lack of significant posttraining deviations. These findings suggest that pain interferes with MI processes, preventing the corticospinal excitability facilitation needed to induce use-dependent plasticity. Pain should be carefully considered for rehabilitation programs using MI to restore motor function.
Fine Mapping without Phenotyping: Identification of Selection Targets in Secondary Evolve and Resequence Experiments
Authors: Langmüller Anna Maria , Dolezal Marlies , Schlötterer Christian 
Published: June 2021

Abstract
Evolve and Resequence (E&R) studies investigate the genomic selection response of populations in an Experimental Evolution setup. Despite the popularity of E&R, empirical studies in sexually reproducing organisms typically suffer from an excess of candidate loci due to linkage disequilibrium, and single gene or SNP resolution is the exception rather than the rule. Recently, so-called “secondary E&R” has been suggested as promising experimental follow-up procedure to confirm putatively selected regions from a primary E&R study. Secondary E&R provides also the opportunity to increase mapping resolution by allowing for additional recombination events, which separate the selection target from neutral hitchhikers. Here, we use computer simulations to assess the effect of different crossing schemes, population size, experimental duration, and number of replicates on the power and resolution of secondary E&R. We find that the crossing scheme and population size are crucial factors determining power and resolution of secondary E&R: A simple crossing scheme with few founder lines consistently outcompetes crossing schemes where evolved populations from a primary E&R experiment are mixed with a complex ancestral founder population. Regardless of the experimental design tested, a population size of at least 4,800 individuals, which is roughly five times larger than population sizes in typical E&R studies, is required to achieve a power of at least 75%. Our study provides an important step toward improved experimental designs aiming to characterize causative SNPs in Experimental Evolution studies.
Parity predicts allonursing in a cooperative breeder
Authors: Brachet Morgane A A , Vullioud Philippe , Ganswindt Andre , Manser Marta B , Keller Matthieu , Clutton-Brock Tim H 
Published: June 2021

Abstract
In some mammals that breed cooperatively, nonbreeding female helpers nurse offspring born to the breeding female in their group, a process known as allonursing. Previous laboratory studies have suggested that primiparous and multiparous females (those that have successfully given birth once or more, respectively) are more likely to contribute to allonursing than nulliparous females (those that have not given birth). In contrast, few field studies have been able to demonstrate whether breeding experience, or parity, affects the likelihood or duration of allonursing. In this study, we investigated whether the likelihood and duration of allonursing by subordinate female meerkats (Suricata suricatta) were associated with variations in their parity (number of pregnancies reaching a viable gestational age) and their immediate pregnancy status. Comparisons showed that nonpregnant nulliparous females were less likely to allonurse than nonpregnant primiparous and multiparous females, although parity was not related to variation in allonursing duration. Parity may enhance the expression of maternal behavior when exposed to foster pups, especially since mammary gland development has been shown to be directly associated with parity in other mammals.
First Record of Established Populations of the Invasive Pathogen Vector and Ectoparasite Haemaphysalis longicornis (Acari: Ixodidae) in Connecticut, United States
Authors: Molaei Goudarz , Little Eliza A H , Williams Scott C , Stafford Kirby C 
Published: June 2021

Abstract
A number of invasive tick species capable of transmitting pathogens have been accidentally introduced into the U.S. in recent years. The invasion and further range expansion of these exotic ticks have been greatly facilitated by frequent global travel and trade as well as increases in legal and illegal importation of animals. We describe the discovery of the first established populations of Haemaphysalis longicornis Neumann and the first fully engorged human parasitizing specimen documented through passive tick surveillance in Fairfield County, Connecticut, U.S. We also report several individual specimens of this invasive arthropod and vector of multiple pathogens of medical and veterinary importance collected through active tick surveillance from three counties (Fairfield, New Haven, and New London). Considering the potential for invasive ticks to transmit numerous native and emerging pathogens, the implementation of comprehensive surveillance programs will aid in prompt interception of these ticks and reduce the risk of infection in humans and wildlife.
#20: Modeling Zika virus tissue tropism in rhesus macaques to define the risk of donor derived transmission
Authors: Treadway Taylor A , Shepherd Phoenix M , Newman Christina M , Mohr Emma L , Dudley Dawn M , Breitbach Meghan E , Yamamoto Keisuke , Stewart Laurel M , Koenig Michelle R , Bliss Mason , Rybarczyk Sierra L , Weiler Andrea M , Semler Matthew R , Mitzey Ann , Razo Elaina , Schotzko Michele , Peterson Eric , Simmons Heather A , Mejia Andres , Golos Thaddeus G , Friedrich Thomas C , O’Connor David H 
Published: June 2021

Abstract

Background
Almost 115,000 people in the United States are currently on a transplant waitlist, which vastly exceeds the number of organ donors every year. This discrepancy emphasizes the need for retention of all possible donors. Those who have recently traveled to an area with an active outbreak of Zika virus (ZIKV) are often disqualified as a donor because immunosuppressed recipients would be at risk of a donor-derived ZIKV infection. Therefore, we define ZIKV tissue tropism and the risk of donor derived transmission.

Methods
We subcutaneously inoculated 15 Indian-origin rhesus macaques (RM) with a Puerto Rican isolate of ZIKV (PRVABC59). All RMs were inoculated in mid to early gestation.We inoculated during pregnancy because plasma viremia is typically prolonged in pregnancy and we wanted to model tissue tropism for donor derived transmission in the worst scenario of prolonged viremia. At 30, 65, and 105 days post-infection (dpi), the animals were euthanized and comprehensive necropsies were performed, which evaluated a minimum of 60 tissues per animal. ZIKV RNA was quantified in tissues via qRT-PCR.

Results
Plasma viremia duration was &gt;10 days in 13 of 15 RMs. ZIKV RNA was most commonly detected in lymph nodes, with 19/45 lymph nodes that were vRNA positive in 5 RMs at 30 dpi. There were 15/45 vRNA positive lymph nodes at 60 dpi and 8/38 at 105 dpi. Reproductive and maternal fetal-interface (MFI) tissues were the second most commonly positive tissues. Twenty-five MFI tissues, including the amniotic/chorionic membrane, decidua, placenta, uterus, and placental bed, were positive, with 10/53 positive at 30 dpi, 14/24 positive at 60 dpi and 1/47 positive at 105 dpi. Other vRNA positive tissues included the primary bronchus, femoral vein, kidney, thyroid, lung, colon, mammary gland, pericardium, hand nerve, and sciatic nerve in 1–2 RMs at one of the three timepoints.

Conclusions
We found ZIKV RNA most frequently within lymph nodes. Lymph nodes are included in lung and small bowel transplants, indicating that these transplants could pose a risk of donor-derived ZIKV transmission. Virus detection within other commonly transplanted tissues, such as the kidney and blood vessels was much less common. We did not determine what fraction of vRNA comes from replication-competent virus in each tissue; some tissues with vRNA might not contain virions that could initiate new infections. Donor-derived Zika virus transmission from other commonly transplanted organs, such as liver, seems unlikely since no viral RNA was detected in this organ.
#52: Clinical Features and Management of Pediatric Patients Presenting with New Onset Acute Leukemia and Concomitant COVID-19
Authors: Patel Pratik A , Lapp Stacey A , Hussaini Laila , Lu Austin , Anderson Evan J , Rostad Christina A , Stokes Claire L , Pauly Melinda G 
Published: June 2021

Abstract

Background
Infections represent a significant cause of morbidity and mortality in pediatric patients undergoing treatment for hematologic malignancies. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has led to a worldwide pandemic of coronavirus disease 2019 (COVID-19) and pediatric patients with cancer appear to be at higher risk of severe disease than reported in the general pediatric population. Data are limited on the optimal management of children infected with SARS-CoV-2 and a new diagnosis of leukemia. The objective of this study was to describe our experience of six children who presented with a new diagnosis of acute leukemia and concurrent COVID-19.

Methods
The study was IRB approved and children were enrolled following informed consent and assent as appropriate for age. The clinical presentations, serologic responses, treatments, and outcomes of patients who presented with acute leukemia and concurrent SARS-CoV-2 infection were abstracted. Residual blood was tested by ELISA for quantitative IgG to the SARS-CoV-2 spike protein receptor binding domain (RBD).

Results
From March 1, 2020 to Dec 31, 2020, 6 patients were identified with a new diagnosis of acute leukemia and SARS-CoV-2 infection including 3 with acute myeloid leukemia (AML) and 3 with acute lymphoblastic leukemia (ALL). The median age of our cohort was 9 years old (range 1 to 19 years old), 5 of 6 were male, and 4 of 6 patients were Hispanic. All 6 patients presented with symptoms that could be attributed to COVID-19 or acute leukemia, with fever being the most common. All 3 of the AML patients presented with hyperleukocytosis (white blood cell count &gt; 50 x 109/L) and required oxygen therapy and intensive care. At the time of presentation, all patients with specimens available (n=5) had IgG antibodies to SARS-CoV-2 RBD. All patients received COVID-19 directed therapy, with remdesivir (n=5) and convalescent plasma (n=5) being the most common. Chemotherapy was modified or delayed in 5 of the 6 patients. The patient who received standard AML chemotherapy without awaiting COVID-19 directed treatment had delayed serologic response, delayed viral clearance from the nasopharynx, protracted respiratory failure, and ultimately died. For patients with a 12-week follow-up (n=5), 2 patients with AML had died, and the ALL patients were in remission and continuing their leukemia treatment.

Conclusion
COVID-19 may present concurrently in children with new onset leukemia resulting in severe morbidity and mortality. Our experience adds to growing evidence that children with AML and SARS-CoV-2 infection are at risk for severe COVID-19. Screening for SARS-CoV-2 infection with subsequent delay in chemotherapy and administration of COVID-19 directed therapies should be considered for pediatric patients with newly diagnosed acute leukemia and COVID-19.
#16: Enterovirus D68 Visualized in the Anterior Horn of the Spinal Cord of a Pediatric Patient with Flaccid Paralysis
Authors: Vogt Matthew R , Wright Peter F , Hickey William F , Boyd Kelli L , Crowe James E 
Published: June 2021

Abstract

Background
Acute flaccid myelitis (AFM) is a polio-like paralyzing illness of children. AFM incidence is increasing during every other year outbreaks that occur in the United States simultaneously with outbreaks of enterovirus D68 (EV-D68) infection. Demonstrating that EV-D68 directly causes AFM has been challenging due to rare detection of the virus in the cerebrospinal fluid (CSF) of patients despite frequent detection at nonsterile sites. Murine studies have shown that EV-D68 can infect spinal cord anterior horn motor neurons and cause paralysis, similar to poliovirus. However, a key outstanding question is whether EV-D68 causes AFM in humans by direct viral pathogenesis or by indirect host immunopathogenesis.

Methods
We investigated the pathogenesis of AFM using tissues from a previously reported case of a 5-year-old boy who presented in fall 2008 with four days of progressive limb and voice weakness followed by incontinence, apnea, and death. He had a CSF pleocytosis of 2094/µL with EV-D68 identified in the CSF by sequencing of the VP1 gene. We designed probes for in situ hybridization (ISH) based on this sequence to stain formalin fixed paraffin embedded tissues from his autopsy. For immunohistochemistry (IHC) we used both commercial polyclonal anti-EV-D68 antibodies and our own human monoclonal antibodies that stain virus infected cells in vitro. Immunophenotyping was done by IHC. To analyze gene transcription in the inflammatory transcriptome of these infected areas of spinal cord we used the GeoMx platform from Nanostring.

Results
We identified EV-D68 in the anterior horn of the patient’s spinal cord, corresponding to the location of motor neuron cell bodies. This area was highly inflamed, with an infiltrate of CD8 T cells and many macrophages. Viral RNA (see figure) and viral protein was visualized in motor neurons but not supporting cells using ISH and IHC, respectively. Viral RNA but not viral protein was detected rarely in the lungs in macrophages, which had extensive inflammatory infiltrate. The infiltrate was predominantly composed of macrophages with a CD8 T cell component as well. The transcriptome of cells in the inflamed tissue was enriched for genes involved in antigen presentation on MHC.

Conclusions
Deaths in AFM patients are rare and often distant from initial presentation, but this patient died four days after onset of weakness, allowing us to directly demonstrate that EV-D68 can infect the human spinal cord. Motor neurons but not neural support cells are directly infected by EV-D68 with a corresponding infiltrate of macrophages and CD8 T cells. Antigen presentation processes are upregulated in inflamed tissues. Therefore, both direct viral pathology and immune factors likely contribute to AFM disease in EV-D68 infection.