bluuebunny/crossref_metadata_2025_split huggingface dataset:
A study of transposable element-associated structural variations (TASVs) using a de novo-assembled Korean genome
Authors: Mun Seyoung , Kim Songmi , Lee Wooseok , Kang Keunsoo , Meyer Thomas J. , Han Bok-Ghee , Han Kyudong , Kim Heui-Soo 
Published: April 2021

AbstractAdvances in next-generation sequencing (NGS) technology have made personal genome sequencing possible, and indeed, many individual human genomes have now been sequenced. Comparisons of these individual genomes have revealed substantial genomic differences between human populations as well as between individuals from closely related ethnic groups. Transposable elements (TEs) are known to be one of the major sources of these variations and act through various mechanisms, including de novo insertion, insertion-mediated deletion, and TE–TE recombination-mediated deletion. In this study, we carried out de novo whole-genome sequencing of one Korean individual (KPGP9) via multiple insert-size libraries. The de novo whole-genome assembly resulted in 31,305 scaffolds with a scaffold N50 size of 13.23 Mb. Furthermore, through computational data analysis and experimental verification, we revealed that 182 TE-associated structural variation (TASV) insertions and 89 TASV deletions contributed 64,232 bp in sequence gain and 82,772 bp in sequence loss, respectively, in the KPGP9 genome relative to the hg19 reference genome. We also verified structural differences associated with TASVs by comparative analysis with TASVs in recent genomes (AK1 and TCGA genomes) and reported their details. Here, we constructed a new Korean de novo whole-genome assembly and provide the first study, to our knowledge, focused on the identification of TASVs in an individual Korean genome. Our findings again highlight the role of TEs as a major driver of structural variations in human individual genomes.
Long-term effects of human induced pluripotent stem cell-derived retinal cell transplantation in Pde6b knockout rats
Authors: Yang Jee Myung , Chung Sunho , Yun KyungA , Kim Bora , So Seongjun , Kang Seoon , Kang Eunju , Lee Joo Yong 
Published: April 2021

AbstractRetinal degenerative disorders, including age-related macular degeneration and retinitis pigmentosa (RP), are characterized by the irreversible loss of photoreceptor cells and retinal pigment epithelial (RPE) cells; however, the long-term effect of implanting both human induced pluripotent stem cell (hiPSC)-derived RPE and photoreceptor for retinal regeneration has not yet been investigated. In this study, we evaluated the long-term effects of hiPSC-derived RPE and photoreceptor cell transplantation in Pde6b knockout rats to study RP; cells were injected into the subretinal space of the right eyes of rats before the appearance of signs of retinal degeneration at 2–3 weeks of age. Ten months after transplantation, we evaluated the cells using fundus photography, optical coherence tomography, and histological evaluation, and no abnormal cell proliferation was observed. A relatively large number of transplanted cells persisted during the first 4 months; subsequently, the number of these cells decreased gradually. Notably, immunohistochemical analysis revealed that the hiPSC-derived retinal cells showed characteristics of both RPE cells and photoreceptors of human origin after transplantation. Functional analysis of vision by scotopic electroretinogram revealed significant preservation of vision after transplantation. Our study suggests that the transplantation of hiPSC-derived retinal cells, including RPE cells and photoreceptors, has a potential therapeutic effect against irreversible retinal degenerative diseases.
Tailoring photosensitive ROS for advanced photodynamic therapy
Authors: Sai Duc Loc , Lee Jieun , Nguyen Duc Long , Kim Young-Pil 
Published: April 2021

AbstractPhotodynamic therapy (PDT) has been considered a noninvasive and cost-effective modality for tumor treatment. However, the complexity of tumor microenvironments poses challenges to the implementation of traditional PDT. Here, we review recent advances in PDT to resolve the current problems. Major breakthroughs in PDTs are enabling significant progress in molecular medicine and are interconnected with innovative strategies based on smart bio/nanomaterials or therapeutic insights. We focus on newly developed PDT strategies designed by tailoring photosensitive reactive oxygen species generation, which include the use of proteinaceous photosensitizers, self-illumination, or oxygen-independent approaches. While these updated PDT platforms are expected to enable major advances in cancer treatment, addressing future challenges related to biosafety and target specificity is discussed throughout as a necessary goal to expand the usefulness of PDT.
One-year outcomes after treatment with a drug-coated balloon catheter system for lower urinary tract symptoms related to benign prostatic hyperplasia
Authors: Kaplan Steven A. , Pichardo Merycarla , Rijo Edwin , Espino Gustavo , Lay Ramon Rodriguez , Estrella Rafael 
Published: April 2021

Abstract
Background
This is the first report of the 1-year outcomes of the EVEREST-I study evaluating the safety and efficacy of the Optilume® BPH Catheter System, a prostatic paclitaxel-coated balloon catheter system, for the treatment of lower urinary tract symptoms (LUTS) related to benign prostatic hyperplasia (BPH).

Methods
Subjects were men >50 years old with moderate-to-severe LUTS secondary to BPH, peak urinary flow rate of 5–15 ml/s, prostatic urethra length 30–55 mm, and prostate volume 20–80 g. All were treated with the Optilume BPH Catheter System and followed at Foley removal, 2 weeks, 30 days, 3, 6, and 12 months after treatment. The primary endpoint was the proportion of subjects with ≥40% improvement in International Prostate Symptom Score (IPSS). The rate of post-procedural complications was evaluated.

Results
Eighty subjects were treated at six sites in Latin America and 75 completed the 1-year follow-up. The percent of subjects with an improvement ≥40% in IPSS from baseline was 81% at 3 months and 1 year. IPSS improved from 22.3 at baseline to 7.9 at 1 year, Qmax improved from 10.9 to 18.4 ml/s, and IPSS QoL improved from 4.6 to 1.3. Post-procedural complications included common urologic events and the rate of complications was significantly impacted by device diameter.

Conclusions
Treatment with the minimally invasive Optilume BPH Catheter System is safe and showed subjective and objective improvements in LUTS. Benefits were rapid and persisted through 1 year. The initial results warrant further evaluation of this therapy as a treatment option for patients with LUTS related to BPH.
Modeling the ecology of parasitic plasmids
Authors: Lopez Jaime G , Donia Mohamed S , Wingreen Ned S 
Published: April 2021

Abstract
Plasmids are autonomous genetic elements that can be exchanged between microorganisms via horizontal gene transfer (HGT). Despite the central role they play in antibiotic resistance and modern biotechnology, our understanding of plasmids’ natural ecology is limited. Recent experiments have shown that plasmids can spread even when they are a burden to the cell, suggesting that natural plasmids may exist as parasites. Here, we use mathematical modeling to explore the ecology of such parasitic plasmids. We first develop models of single plasmids and find that a plasmid’s population dynamics and optimal infection strategy are strongly determined by the plasmid’s HGT mechanism. We then analyze models of co-infecting plasmids and show that parasitic plasmids are prone to a “tragedy of the commons” in which runaway plasmid invasion severely reduces host fitness. We propose that this tragedy of the commons is averted by selection between competing populations and demonstrate this effect in a metapopulation model. We derive predicted distributions of unique plasmid types in genomes—comparison to the distribution of plasmids in a collection of 17,725 genomes supports a model of parasitic plasmids with positive plasmid–plasmid interactions that ameliorate plasmid fitness costs or promote the invasion of new plasmids.
Spontaneous and deliberate creative cognition during and after psilocybin exposure
Authors: Mason N. L. , Kuypers K. P. C. , Reckweg J. T. , Müller F. , Tse D. H. Y. , Da Rios B. , Toennes S. W. , Stiers P. , Feilding A. , Ramaekers J. G. 
Published: April 2021

AbstractCreativity is an essential cognitive ability linked to all areas of our everyday functioning. Thus, finding a way to enhance it is of broad interest. A large number of anecdotal reports suggest that the consumption of psychedelic drugs can enhance creative thinking; however, scientific evidence is lacking. Following a double-blind, placebo-controlled, parallel-group design, we demonstrated that psilocybin (0.17 mg/kg) induced a time- and construct-related differentiation of effects on creative thinking. Acutely, psilocybin increased ratings of (spontaneous) creative insights, while decreasing (deliberate) task-based creativity. Seven days after psilocybin, number of novel ideas increased. Furthermore, we utilized an ultrahigh field multimodal brain imaging approach, and found that acute and persisting effects were predicted by within- and between-network connectivity of the default mode network. Findings add some support to historical claims that psychedelics can influence aspects of the creative process, potentially indicating them as a tool to investigate creativity and subsequent underlying neural mechanisms. Trial NL6007; psilocybin as a tool for enhanced cognitive flexibility;https://www.trialregister.nl/trial/6007.
The anatomy of past abrupt warmings recorded in Greenland ice
Authors: Capron E. , Rasmussen S. O. , Popp T. J. , Erhardt T. , Fischer H. , Landais A. , Pedro J. B. , Vettoretti G. , Grinsted A. , Gkinis V. , Vaughn B. , Svensson A. , Vinther B. M. , White J. W. C. 
Published: April 2021

AbstractData availability and temporal resolution make it challenging to unravel the anatomy (duration and temporal phasing) of the Last Glacial abrupt climate changes. Here, we address these limitations by investigating the anatomy of abrupt changes using sub-decadal-scale records from Greenland ice cores. We highlight the absence of a systematic pattern in the anatomy of abrupt changes as recorded in different ice parameters. This diversity in the sequence of changes seen in ice-core data is also observed in climate parameters derived from numerical simulations which exhibit self-sustained abrupt variability arising from internal atmosphere-ice-ocean interactions. Our analysis of two ice cores shows that the diversity of abrupt warming transitions represents variability inherent to the climate system and not archive-specific noise. Our results hint that during these abrupt events, it may not be possible to infer statistically-robust leads and lags between the different components of the climate system because of their tight coupling.
Role of DegQ in differential stability of flagellin subunits in Vibrio vulnificus
Authors: Jung You-Chul , Lee Mi-Ae , Kim Han-Shin , Lee Kyu-Ho 
Published: April 2021

AbstractBiofilm formation of Vibrio vulnificus is initiated by adherence of flagellated cells to surfaces, and then flagellum-driven motility is not necessary during biofilm maturation. Once matured biofilms are constructed, cells become flagellated and swim to disperse from biofilms. As a consequence, timely regulations of the flagellar components’ expression are crucial to complete a biofilm life-cycle. In this study, we demonstrated that flagellins’ production is regulated in a biofilm stage-specific manner, via activities of a protease DegQ and a chaperone FlaJ. Among four flagellin subunits for V. vulnificus filament, FlaC had the highest affinities to hook-associated proteins, and is critical for maturating flagellum, showed the least susceptibility to DegQ due to the presence of methionine residues in its DegQ-sensitive domains, ND1 and CD0. Therefore, differential regulation by DegQ and FlaJ controls the cytoplasmic stability of flagellins, which further determines the motility-dependent, stage-specific development of biofilms.
A thermodynamic platform for evaluating the energy efficiency of combined power generation and desalination plants
Authors: Ng Kim Choon , Burhan Muhammad , Chen Qian , Ybyraiymkul Doskhan , Akhtar Faheem Hassan , Kumja M. , Field Robert W. , Shahzad Muhammad Wakil 
Published: April 2021

AbstractIn seawater desalination, the energy efficiency of practical processes is expressed in kWh_electricity or low-grade-heat per m3 of water produced, omitting the embedded energy quality underlying their generation processes. To avoid thermodynamic misconceptions, it is important to recognize both quality and quantity of energy consumed. An unmerited quantitative apportionment can result in inferior deployment of desalination methods. This article clarifies misapprehensions regarding seeming parity between electricity and thermal sources that are sequentially cogenerated in power plants. These processes are represented by heat engines to yield the respective maximum (Carnot) work potentials. Equivalent work from these engines are normalized individually to give a corresponding standard primary energy (QSPE), defined via a common energy platform between the adiabatic flame temperature of fuel and the surroundings. Using the QSPE platform, the energy efficiency of 60 desalination plants of assorted types, available from literature, are compared retrospectively and with respect to Thermodynamic Limit.
Digital image processing to detect subtle motion in stony coral
Authors: Li Shuaifeng , Roger Liza M. , Kumar Lokender , Lewinski Nastassja A. , Klein-Seetharaman Judith , Gagnon Alex , Putnam Hollie M. , Yang Jinkyu 
Published: April 2021

AbstractCoral reef ecosystems support significant biological activities and harbor huge diversity, but they are facing a severe crisis driven by anthropogenic activities and climate change. An important behavioral trait of the coral holobiont is coral motion, which may play an essential role in feeding, competition, reproduction, and thus survival and fitness. Therefore, characterizing coral behavior through motion analysis will aid our understanding of basic biological and physical coral functions. However, tissue motion in the stony scleractinian corals that contribute most to coral reef construction are subtle and may be imperceptible to both the human eye and commonly used imaging techniques. Here we propose and apply a systematic approach to quantify and visualize subtle coral motion across a series of light and dark cycles in the scleractinian coral Montipora capricornis. We use digital image correlation and optical flow techniques to quantify and characterize minute coral motions under different light conditions. In addition, as a visualization tool, motion magnification algorithm magnifies coral motions in different frequencies, which explicitly displays the distinctive dynamic modes of coral movement. Specifically, our assessment of displacement, strain, optical flow, and mode shape quantify coral motion under different light conditions, and they all show that M. capricornis exhibits more active motions at night compared to day. Our approach provides an unprecedented insight into micro-scale coral movement and behavior through macro-scale digital imaging, thus offering a useful empirical toolset for the coral research community.
Three-dimensional (3D) polymer—metal–carbon framework for efficient removal of chemical and biological contaminants
Authors: Sasidharan V , Sachan Deepa , Chauhan Divya , Talreja Neetu , Ashfaq Mohammad 
Published: April 2021

AbstractThe continuously increased existence of contaminants such as chemical and biological mainly dye, bacteria, and heavy metals ions (HMI) in water bodies has increased environmental concern due to their hostile effects on living things. Therefore, there is necessity to be developed newer materials that skirmishes such environmental menace. The present works focus on the synthesis of a novel three-dimensional (3D) polymer-metal–carbon (3D-PMC) framework for the exclusion of contaminants (chemical and biological) from water bodies. Initially, polyurethane (PU) foam was treated with nitric acid and used as a framework for the development of 3D-PMC materials. The copper nanosheet (Cu-NS) was deposited onto the functionalized PU foam to produce Cu-NS-PU material. The mechanically exfoliated graphene was mixed with chitosan to produce a graphene-chitosan homogenous suspension. The produce homogenous suspension was deposited Cu-NS-PU for the development of the 3D-PMC framework. The prepared 3D-PMC framework was characterized by scanning electron microscopy (SEM), Energy Dispersive X-Ray Analysis (EDX), Fourier-transform infrared spectroscopy (FT-IR), and X-rays diffraction (XRD) analysis. The prepared 3D-PMC framework was subjected to various adsorption parameters to assess the sorption ability of the material. The prepared 3D-PMC framework was effectively used for the removal of chromium (Cr) metal ions and Congo-red (CR) dye from the water system. The synthesis of the 3D-PMC framework is simple, novel, cost-effective, and economically viable. Therefore, the prepared 3D-PMC framework has the potential to be used as a filter assembly in water treatment technologies.
Spatial distribution and risk factors of adverse treatment outcomes of tuberculosis in Guizhou, China, 2013–2018
Authors: Zhou Jian , Ma Xiaoxue , Tian Juan , Hong Feng , Li Jinlan 
Published: April 2021

AbstractThe incidence of Tuberculosis (TB) in Guizhou province has ranked to be the top four among the 31 China provinces. The spatial distribution and influencing factors of adverse outcomes of TB in Guizhou are unclear. In our study, the cases information of TB in Guizhou province from 2013 to 2018 was collected, we analyzed the spatial distribution and clusters of five adverse outcomes of TB with ArcMap10.2 software, used logistics regression analysis to assessed risk factors and used Chi-square analysis to analyze variation trend of the five adverse outcomes. A total of 237, 806 cases information of TB were collected. The proportion of adverse outcomes in TB patients was 6.18%, among which adverse reactions accounted for 1.05%, lost to follow-up accounted for 1.44%, treatment failed accounted for 1.15%, died accounted for 2.31%, switch to MDR accounted for 0.24%. The component ratio of adverse outcomes showed an upward trend (P < 0.05).Regional clustering existed in each of adverse outcomes (P < 0.05). There were high-risk minorities, gender, age, occupation, type of diagnosis, Therapeutic category existed in adverse outcomes of TB. Miao and Dong had a higher risk in adverse reaction of TB compared with Han. Women had a higher risk in adverse reactions than men, and a lower risk of lost to follow-up, failed, and died. Retreated patients had a higher risk of adverse outcomes. Timely monitoring and active intervention should be carried out for some high-risk areas and groups, including middle-aged and elderly patients, rural patients, floating patients, severe patients and retreated patients during the process of patient diagnosis and treatment.
A decade-long silent ground subsidence hazard culminating in a metropolitan disaster in Maceió, Brazil
Authors: Vassileva Magdalena , Al-Halbouni Djamil , Motagh Mahdi , Walter Thomas R. , Dahm Torsten , Wetzel Hans-Ulrich 
Published: April 2021

AbstractGround subsidence caused by natural or anthropogenic processes affects major urban areas worldwide. Sinkhole formation and infrastructure fractures have intensified in the federal capital of Maceió (Alagoas, Brazil) since early 2018, forcing authorities to relocate affected residents and place buildings under demolition. In this study, we present a 16-year history (2004–2020) of surface displacement, which shows precursory deformations in 2004–2005, reaching a maximum cumulative subsidence of approximately 200 cm near the Mundaú Lagoon coast in November 2020. By integrating the displacement observations with numerical source modelling, we suggest that extensive subsidence can be primarily associated with the removal of localized, deep-seated material at the location and depth where salt is mined. We discuss the accelerating subsidence rates, influence of severe precipitation events on the aforementioned geological instability, and related hazards. This study suggests that feedback destabilization mechanisms may arise in evaporite systems due to anthropogenic activities, fostering enhanced and complex superficial ground deformation.
Predicting the clinical management of skin lesions using deep learning
Authors: Abhishek Kumar , Kawahara Jeremy , Hamarneh Ghassan 
Published: April 2021

AbstractAutomated machine learning approaches to skin lesion diagnosis from images are approaching dermatologist-level performance. However, current machine learning approaches that suggest management decisions rely on predicting the underlying skin condition to infer a management decision without considering the variability of management decisions that may exist within a single condition. We present the first work to explore image-based prediction of clinical management decisions directly without explicitly predicting the diagnosis. In particular, we use clinical and dermoscopic images of skin lesions along with patient metadata from the Interactive Atlas of Dermoscopy dataset (1011 cases; 20 disease labels; 3 management decisions) and demonstrate that predicting management labels directly is more accurate than predicting the diagnosis and then inferring the management decision ($$13.73 \pm 3.93\%$$

13.73
±
3.93
%

and $$6.59 \pm 2.86\%$$

6.59
±
2.86
%

improvement in overall accuracy and AUROC respectively), statistically significant at $$p < 0.001$$

p
<
0.001

. Directly predicting management decisions also considerably reduces the over-excision rate as compared to management decisions inferred from diagnosis predictions (24.56% fewer cases wrongly predicted to be excised). Furthermore, we show that training a model to also simultaneously predict the seven-point criteria and the diagnosis of skin lesions yields an even higher accuracy (improvements of $$4.68 \pm 1.89\%$$

4.68
±
1.89
%

and $$2.24 \pm 2.04\%$$

2.24
±
2.04
%

in overall accuracy and AUROC respectively) of management predictions. Finally, we demonstrate our model’s generalizability by evaluating on the publicly available MClass-D dataset and show that our model agrees with the clinical management recommendations of 157 dermatologists as much as they agree amongst each other.
Rethinking GPS navigation: creating cognitive maps through auditory clues
Authors: Clemenson Gregory D. , Maselli Antonella , Fiannaca Alexander J. , Miller Amos , Gonzalez-Franco Mar 
Published: April 2021

AbstractGPS navigation is commonplace in everyday life. While it has the capacity to make our lives easier, it is often used to automate functions that were once exclusively performed by our brain. Staying mentally active is key to healthy brain aging. Therefore, is GPS navigation causing more harm than good? Here we demonstrate that traditional turn-by-turn navigation promotes passive spatial navigation and ultimately, poor spatial learning of the surrounding environment. We propose an alternative form of GPS navigation based on sensory augmentation, that has the potential to fundamentally alter the way we navigate with GPS. By implementing a 3D spatial audio system similar to an auditory compass, users are directed towards their destination without explicit directions. Rather than being led passively through verbal directions, users are encouraged to take an active role in their own spatial navigation, leading to more accurate cognitive maps of space. Technology will always play a significant role in everyday life; however, it is important that we actively engage with the world around us. By simply rethinking the way we interact with GPS navigation, we can engage users in their own spatial navigation, leading to a better spatial understanding of the explored environment.