bluuebunny/crossref_metadata_2025_split huggingface dataset:
Implementation of geriatric assessment and long-term care insurance system by medical professionals in cancer treatment: a nationwide survey in Japan
Authors: Yoshida Yoichiro , Tamura Kazuo ,   the Geriatric Oncology Guideline-establishing Study Group
Published: February 2022

Abstract

Background
A questionnaire survey was conducted to assess the implementation status of geriatric assessment in cancer treatment and the potential for collaboration between medical care and the long-term care insurance system.

Methods
Questionnaires were sent to 795 facilities in Japan. The questions were instructed to be answered via an online survey (SurveyMonkey®), which began in September 2020 and closed on 31 October 2020. The questionnaire consisted of 8 questions on the status of geriatric assessment implementation and 15 questions on the long-term care insurance system.

Results
In total, 631 departments in 340 (42.8%) of 795 hospitals and clinics provided responses. Approximately 81.5% of the departments did not perform geriatric assessment. The common reasons were lack of knowledge about geriatric assessment (54.0%) and lack of personnel (35.5%). Even if geriatric assessment was conducted, 63.6% of departments did not utilize geriatric assessment results in clinical practice. Approximately 61.7% of respondents were familiar with the long-term care insurance system and 62.9% with the certification process. Moreover, 28% of respondents used certification examination results in treatment planning.

Conclusions
Geriatric assessment is less recognized than the long-term care insurance system, and its results are rarely used in clinical practice. However, 28% of certification examination results are utilized in treatment decision-making. Notably, this survey first showed the incorporation of the long-term care insurance system into the medical care of vulnerable elderly patients with cancer.
Laparoscopic reduction of intersigmoid hernia: early surgical intervention for a rare form of internal hernia
Authors: Youn Sang Il , Kim Dong-Wook , Jee Ye Seob 
Published: February 2022

Abstract
Intersigmoid hernia is a rare form of internal hernia presenting with symptoms of bowel obstruction. A 32-year-old male visited the emergency department with chief complaint of abrupt onset of abdominal pain without any history of prior abdominal surgery. The initial abdominal X-ray and computed tomography (CT) scan exhibited mild distension of small bowel and paralytic ileus with no definitive obstruction site. However, a 12-h follow-up abdominal X-ray showed manifestations of newly appeared step-ladder sign and the CT scan displayed mechanical obstruction in the left lower quadrant area. Upon laparoscopic examination, herniation of small bowel was observed through the intersigmoid recess. Reduction was performed for about 5 cm of incarcerated ileum, and there was no sign of necrosis or lasting damage. The patient was discharged without complications. Laparoscopic management of intersigmoid hernia is possible with early surgical management of mechanical obstruction.
Contributions of sugar transporters to crop yield and fruit quality
Authors: Wen Suying , Neuhaus H Ekkehard , Cheng Jintao , Bie Zhilong 
Published: February 2022

Abstract
The flux, distribution, and storage of soluble sugars regulate crop yield in terms of starch, oil, protein, and total carbohydrates, and affect the quality of many horticultural products. Sugar transporters contribute to phloem loading and unloading. The mechanisms of phloem loading have been studied in detail, but the complex and diverse mechanisms of phloem unloading and sugar storage in sink organs are less explored. Unloading and subsequent transport mechanisms for carbohydrates vary in different sink organs. Analyzing the transport and storage mechanisms of carbohydrates in important storage organs, such as cereal seeds, fruits, or stems of sugarcane, will provide information for genetic improvements to increase crop yield and fruit quality. This review discusses current research progress on sugar transporters involved in carbohydrate unloading and storage in sink organs. The roles of sugar transporters in crop yield and the accumulation of sugars are also discussed to highlight their contribution to efficient breeding.
Value of Thyroid Peroxidase Antibodies in Neuroimmune Diseases: Analysis of Interference During Treatment with Intravenous Immunoglobulins
Authors: Jiménez-Legido María , Cantarín-Extremera Verónica , López-Guio María Eugenia , González-Cervera Rosa María , Martín-Prado Silvia , Sebastián-Pérez Elena , González-Gutiérrez-Solana Luis 
Published: February 2022

Abstract

Objective
The absence of specific markers can make the diagnosis of neuroimmune disorders difficult, making other biomarkers such as thyroid peroxidase antibodies (TPO-Abs) more relevant. Laboratory tests are susceptible to interference, especially those tests performed using immunoassay techniques. The effect of treatment with human intravenous immunoglobulin (IVIG) on the results of TPO-Abs assays has not been previously characterized.

Materials and Methods
We analyzed TPO-Abs levels in 170 children monitored in the neuroimmune disease department of a tertiary hospital. We analyzed the characteristics of patients with increased TPO-Abs values and compared their progress with and without treatment.

Results
We found that 97% of patients with elevated TPO-Abs had received IVIG. After withdrawal from IVIG, a mean TPO-Abs decrease of 62.5% at 1 month was observed. The IVIG drug preparation was found to contain 1176 U/mL of TPO-Abs. An interferogram confirmed interference.

Conclusion
It is advisable to measure levels of TPO-Abs before starting immunotherapy and remain vigilant regarding possible interference in the event of unsubstantiated elevations of this analyte.
Estimating the local dark matter density in a non-axisymmetric wobbling disc
Authors: Sivertsson S , Read J I , Silverwood H , de Salas P F , Malhan K , Widmark A , Laporte C F P , Garbari S , Freese K 
Published: February 2022

ABSTRACT
The density of dark matter near the Sun, ρDM, ⊙, is important for experiments hunting for dark matter particles in the laboratory, and for constraining the local shape of the Milky Way’s dark matter halo. Estimates to date have typically assumed that the Milky Way’s stellar disc is axisymmetric and in a steady-state. Yet the Milky Way disc is neither, exhibiting prominent spiral arms and a bar, and vertical and radial oscillations. We assess the impact of these assumptions on determinations of ρDM, ⊙ by applying a free-form, steady-state, Jeans method to two different N-body simulations of Milky Way-like galaxies. In one, the galaxy has experienced an ancient major merger, similar to the hypothesized Gaia–Sausage–Enceladus; in the other, the galaxy is perturbed more recently by the repeated passage and slow merger of a Sagittarius-like dwarf galaxy. We assess the impact of each of the terms in the Jeans–Poisson equations on our ability to correctly extract ρDM, ⊙ from the simulated data. We find that common approximations employed in the literature – axisymmetry and a locally flat rotation curve – can lead to significant systematic errors of up to a factor ∼1.5 in the recovered surface mass density ∼2 kpc above the disc plane, implying a fractional error on ρDM, ⊙ of the order of unity. However, once we add in the tilt term and the rotation curve term in our models, we obtain an unbiased estimate of ρDM, ⊙, consistent with the true value within our 95 per cent confidence intervals for realistic 20 per cent uncertainties on the baryonic surface density of the disc. Other terms – the axial tilt, 2nd Poisson and time-dependent terms – contribute less than 10 per cent to ρDM, ⊙ (given current data) and can be safely neglected for now. In the future, as more data become available, these terms will need to be included in the analysis.
Superdiffusion of cosmic rays in compressible magnetized turbulence
Authors: Hu Yue , Lazarian A , Xu Siyao 
Published: February 2022

ABSTRACT
Owing to the complexity of turbulent magnetic fields, modelling the diffusion of cosmic rays is challenging. Based on the current understanding of anisotropic magnetohydrodynamic (MHD) turbulence, we use test particles to examine the cosmic rays’ superdiffusion in the direction perpendicular to the mean magnetic field. By changing Alfvén Mach number MA and sonic Mach number MS of compressible MHD simulations, our study covers a wide range of astrophysical conditions including subsonic warm gas phase and supersonic cold molecular gas. We show that freely streaming cosmic rays’ perpendicular displacement increases as 3/2 to the power of the time travelled along local magnetic field lines. This power-law index changes to 3/4 if the parallel propagation is diffusive. We find that the cosmic rays’ parallel mean free path decreases in a power-law relation of $M_\mathrm{ A}^{-2}$ in supersonic turbulence. We investigate the energy fraction of slow, fast, and Alfvénic modes and confirm the dominance of Alfvénic modes in the perpendicular superdiffusion. In particular, the energy fraction of fast mode, which is the main agent for pitch-angle scattering, increases with MA, but is insensitive to MS ≥ 2. Accordingly, our results suggest that the suppressed diffusion in supersonic molecular clouds arises primarily due to the variations of MA instead of MS.
The Carbon Footprint of Bioinformatics
Authors: Grealey Jason , Lannelongue Loïc , Saw Woei-Yuh , Marten Jonathan , Méric Guillaume , Ruiz-Carmona Sergio , Inouye Michael 
Published: February 2022

AbstractBioinformatic research relies on large-scale computational infrastructures which have a nonzero carbon footprint but so far, no study has quantified the environmental costs of bioinformatic tools and commonly run analyses. In this work, we estimate the carbon footprint of bioinformatics (in kilograms of CO2 equivalent units, kgCO2e) using the freely available Green Algorithms calculator (www.green-algorithms.org, last accessed 2022). We assessed 1) bioinformatic approaches in genome-wide association studies (GWAS), RNA sequencing, genome assembly, metagenomics, phylogenetics, and molecular simulations, as well as 2) computation strategies, such as parallelization, CPU (central processing unit) versus GPU (graphics processing unit), cloud versus local computing infrastructure, and geography. In particular, we found that biobank-scale GWAS emitted substantial kgCO2e and simple software upgrades could make it greener, for example, upgrading from BOLT-LMM v1 to v2.3 reduced carbon footprint by 73%. Moreover, switching from the average data center to a more efficient one can reduce carbon footprint by approximately 34%. Memory over-allocation can also be a substantial contributor to an algorithm’s greenhouse gas emissions. The use of faster processors or greater parallelization reduces running time but can lead to greater carbon footprint. Finally, we provide guidance on how researchers can reduce power consumption and minimize kgCO2e. Overall, this work elucidates the carbon footprint of common analyses in bioinformatics and provides solutions which empower a move toward greener research.
Comparative Genomics Elucidates the Origin of a Supergene Controlling Floral Heteromorphism
Authors: Potente Giacomo , Léveillé-Bourret Étienne , Yousefi Narjes , Choudhury Rimjhim Roy , Keller Barbara , Diop Seydina Issa , Duijsings Daniël , Pirovano Walter , Lenhard Michael , Szövényi Péter , Conti Elena 
Published: February 2022

AbstractSupergenes are nonrecombining genomic regions ensuring the coinheritance of multiple, coadapted genes. Despite the importance of supergenes in adaptation, little is known on how they originate. A classic example of supergene is the S locus controlling heterostyly, a floral heteromorphism occurring in 28 angiosperm families. In Primula, heterostyly is characterized by the cooccurrence of two complementary, self-incompatible floral morphs and is controlled by five genes clustered in the hemizygous, ca. 300-kb S locus. Here, we present the first chromosome-scale genome assembly of any heterostylous species, that of Primula veris (cowslip). By leveraging the high contiguity of the P. veris assembly and comparative genomic analyses, we demonstrated that the S-locus evolved via multiple, asynchronous gene duplications and independent gene translocations. Furthermore, we discovered a new whole-genome duplication in Ericales that is specific to the Primula lineage. We also propose a mechanism for the origin of S-locus hemizygosity via nonhomologous recombination involving the newly discovered two pairs of CFB genes flanking the S locus. Finally, we detected only weak signatures of degeneration in the S locus, as predicted for hemizygous supergenes. The present study provides a useful resource for future research addressing key questions on the evolution of supergenes in general and the S locus in particular: How do supergenes arise? What is the role of genome architecture in the evolution of complex adaptations? Is the molecular architecture of heterostyly supergenes across angiosperms similar to that of Primula?
The BlueScreen HC assay to predict the genotoxic potential of fragrance materials
Authors: Thakkar Yax , Joshi Kaushal , Hickey Christina , Wahler Joseph , Wall Brian , Etter Sylvain , Smith Benjamin , Griem Peter , Tate Matthew , Jones Frank , Oudraogo Gladys , Pfuhler Stefan , Choi Christopher , Williams Gary , Greim Helmut , Eisenbrand Gerhard , Dekant Wolfgang , Api Anne Marie 
Published: February 2022

Abstract
BlueScreen HC is a mammalian cell-based assay for measuring the genotoxicity and cytotoxicity of chemical compounds and mixtures. The BlueScreen HC assay has been utilized at the Research Institute for Fragrance Materials in a safety assessment program as a screening tool to prioritize fragrance materials for higher-tier testing, as supporting evidence when using a read-across approach, and as evidence to adjust the threshold of toxicological concern. Predictive values for the BlueScreen HC assay were evaluated based on the ability of the assay to predict the outcome of in vitro and in vivo mutagenicity and chromosomal damage genotoxicity assays. A set of 371 fragrance materials was assessed in the BlueScreen HC assay along with existing or newly generated in vitro and in vivo genotoxicity data. Based on a weight-of-evidence approach, the majority of materials in the data set were deemed negative and concluded not to have the potential to be genotoxic, while only a small proportion of materials were determined to show genotoxic effects in these assays. Analysis of the data set showed a combination of high positive agreement but low negative agreement between BlueScreen HC results, in vitro regulatory genotoxicity assays, and higher-tier test results. The BlueScreen HC assay did not generate any false negatives, thereby providing robustness when utilizing it as a high-throughput screening tool to evaluate the large inventory of fragrance materials. From the perspective of protecting public health, it is desirable to have no or minimal false negatives, as a false-negative result may incorrectly indicate the lack of a genotoxicity hazard. However, the assay did have a high percentage of false-positive results, resulting in poor positive predictivity of the in vitro genotoxicity test battery outcome. Overall, the assay generated 100% negative predictivity and 3.9% positive predictivity. In addition to the data set of 371 fragrance materials, 30 natural complex substances were evaluated for BlueScreen HC, Ames, and in vitro micronucleus assay, and a good correlation in all three assays was observed. Overall, while a positive result may have to be further investigated, these findings suggest that the BlueScreen HC assay can be a valuable screening tool to detect the genotoxic potential of fragrance materials and mixtures.
Non-equilibrium structural dynamics of supercoiled DNA plasmids exhibits asymmetrical relaxation
Authors: Shaheen Cynthia , Hastie Cameron , Metera Kimberly , Scott Shane , Zhang Zhi , Chen Sitong , Gu Gracia , Weber Lisa , Munsky Brian , Kouzine Fedor , Levens David , Benham Craig , Leslie Sabrina 
Published: February 2022

Abstract
Many cellular processes occur out of equilibrium. This includes site-specific unwinding in supercoiled DNA, which may play an important role in gene regulation. Here, we use the Convex Lens-induced Confinement (CLiC) single-molecule microscopy platform to study these processes with high-throughput and without artificial constraints on molecular structures or interactions. We use two model DNA plasmid systems, pFLIP-FUSE and pUC19, to study the dynamics of supercoiling-induced secondary structural transitions after perturbations away from equilibrium. We find that structural transitions can be slow, leading to long-lived structural states whose kinetics depend on the duration and direction of perturbation. Our findings highlight the importance of out-of-equilibrium studies when characterizing the complex structural dynamics of DNA and understanding the mechanisms of gene regulation.
The transient Spt4-Spt5 complex as an upstream regulator of non-coding RNAs during development
Authors: Owsian Dawid , Gruchota Julita , Arnaiz Olivier , Nowak Jacek K 
Published: February 2022

AbstractThe Spt4-Spt5 complex is conserved and essential RNA polymerase elongation factor. To investigate the role of the Spt4-Spt5 complex in non-coding transcription during development, we used the unicellular model Paramecium tetraurelia. In this organism harboring both germline and somatic nuclei, massive transcription of the entire germline genome takes place during meiosis. This phenomenon starts a series of events mediated by different classes of non-coding RNAs that control developmentally programmed DNA elimination. We focused our study on Spt4, a small zinc-finger protein encoded in P. tetraurelia by two genes expressed constitutively and two genes expressed during meiosis. SPT4 genes are not essential in vegetative growth, but they are indispensable for sexual reproduction, even though genes from both expression families show functional redundancy. Silencing of the SPT4 genes resulted in the absence of double-stranded ncRNAs and reduced levels of scnRNAs – 25 nt-long sRNAs produced from these double-stranded precursors in the germline nucleus. Moreover, we observed that the presence of a germline-specific Spt4-Spt5m complex is necessary for transfer of the scnRNA-binding PIWI protein between the germline and somatic nucleus. Our study establishes that Spt4, together with Spt5m, is essential for expression of the germline genome and necessary for developmental genome rearrangements.
Parathyroid hormone and phosphate homeostasis in patients with Bartter and Gitelman syndrome: an international cross-sectional study
Authors: Verploegen Maartje F A , Vargas-Poussou Rosa , Walsh Stephen B , Alpay Harika , Amouzegar Atefeh , Ariceta Gema , Atmis Bahriye , Bacchetta Justine , Bárány Peter , Baron Stéphanie , Bayrakci Umut Selda , Belge Hendrica , Besouw Martine , Blanchard Anne , Bökenkamp Arend , Boyer Olivia , Burgmaier Kathrin , Calò Lorenzo A , Decramer Stéphane , Devuyst Olivier , van Dyck Maria , Ferraro Pietro Manuel , Fila Marc , Francisco Telma , Ghiggeri Gian Marco , Gondra Leire , Guarino Stefano , Hooman Nakysa , Hoorn Ewout J , Houillier Pascal , Kamperis Konstantinos , Kari Jameela A , Konrad Martin , Levtchenko Elena , Lucchetti Laura , Lugani Francesca , Marzuillo Pierluigi , Mohidin Barian , Neuhaus Thomas J , Osman Abdaldafae , Papizh Svetlana , Perelló Manel , Rookmaaker Maarten B , Conti Valerie Said , Santos Fernando , Sawaf Ghalia , Serdaroglu Erkin , Szczepanska Maria , Taroni Francesca , Topaloglu Rezan , Trepiccione Francesco , Vidal Enrico , Wan Elizabeth R , Weber Lutz , Yildirim Zeynep Yuruk , Yüksel Selçuk , Zlatanova Galia , Bockenhauer Detlef , Emma Francesco , Nijenhuis Tom 
Published: February 2022

ABSTRACT

Background
Small cohort studies have reported high parathyroid hormone (PTH) levels in patients with Bartter syndrome and lower serum phosphate levels have anecdotally been reported in patients with Gitelman syndrome. In this cross-sectional study, we assessed PTH and phosphate homeostasis in a large cohort of patients with salt-losing tubulopathies.

Methods
Clinical and laboratory data of 589 patients with Bartter and Gitelman syndrome were provided by members of the European Rare Kidney Diseases Reference Network (ERKNet) and the European Society for Paediatric Nephrology (ESPN).

Results
A total of 285 patients with Bartter syndrome and 304 patients with Gitelman syndrome were included for analysis. Patients with Bartter syndrome type I and II had the highest median PTH level (7.5 pmol/L) and 56% had hyperparathyroidism (PTH &gt;7.0 pmol/L). Serum calcium was slightly lower in Bartter syndrome type I and II patients with hyperparathyroidism (2.42 versus 2.49 mmol/L; P = .038) compared to those with normal PTH levels and correlated inversely with PTH (rs −0.253; P = .009). Serum phosphate and urinary phosphate excretion did not correlate with PTH. Overall, 22% of patients had low serum phosphate levels (phosphate—standard deviation score &lt; −2), with the highest prevalence in patients with Bartter syndrome type III (32%). Serum phosphate correlated with tubular maximum reabsorption of phosphate/glomerular filtration rate (TmP/GFR) (rs 0.699; P &lt; .001), suggesting renal phosphate wasting.

Conclusions
Hyperparathyroidism is frequent in patients with Bartter syndrome type I and II. Low serum phosphate is observed in a significant number of patients with Bartter and Gitelman syndrome and appears associated with renal phosphate wasting.
Measuring patients’ experience with renal services in the UK: development and validation of the Kidney PREM
Authors: Hawkins Janine , Wellsted David , Corps Claire , Fluck Richard , Gair Rachel , Hall Natalie , Busby Amanda , Rider Beth , Farrington Ken , Sharma Shivani , van der Veer Sabine N 
Published: February 2022

ABSTRACT

Background
Patient experience is a recognized aspect of quality of care for people with chronic kidney disease (CKD), but current patient-reported experience measures (PREMs) only focus on dialysis care. We developed and validated the Kidney PREM to assess patients’ experience with renal services in secondary care for any CKD stage or treatment (transplant, haemodialysis and peritoneal dialysis).

Methods
We developed the Kidney PREM in two phases, informed by a multidisciplinary expert group to ensure face validity. We organized three national data collections (2016–8) to investigate item response profiles and to conduct exploratory and confirmatory analyses to assess internal consistency. We also explored content validity in cognitive interviews and evaluated test–retest reliability. Finally, we developed the Kidney PREM Short Form for more frequent measurement of patient experience to inform local service improvements.

Results
We analysed 32 959 responses across data collections, with the 2018 collection covering all 71 UK renal centres. The Kidney PREM final version consisted of 38 items grouped into 13 themes, all pertaining to one underlying dimension reflecting the construct of ‘patient experience’ with high internal consistency (Cronbach's α = 0.94). The Kidney PREM Short Form consisted of 15 items across the same 13 themes.

Conclusions
The Kidney PREM supports the collection of reliable information on patient experience that people with CKD consider relevant, regardless of CKD stage or treatment modality. Kidney PREM data have the potential to guide local and national initiatives to improve patients’ experiences with renal services in the UK and other countries.