bluuebunny/crossref_metadata_2025_split huggingface dataset:
Efficacy of Biochar-biofertilizer-vermicompost Treatment on Theobroma cacao and Rhizosphere Soil Microbial Population
Authors: Gonzales K K M P , Gestiada E C , Aggangan N S 
Published: February 2023

Abstract
The study investigated the effects of a novel biochar-biofertilizer-vermicompost formulation on the rhizosphere soil microbial community and growth of mature T. cacao trees planted in three farms in the provinces of Batangas (Lipa) and Laguna (Liliw and Magdalena), Philippines. Cacao trees were amended with MYKORICH® (MR) without or with 15% bamboo biochar (15% BB) and vermicompost. In the three years span of the experiment, stem diameter increments of BB-treated cacao in Magdalena and Lipa were 5% and 19% higher than the control (56.09 mm and 49.08 mm), respectively, whereas MR and MR + BB-treated trees in Liliw were 34-35% higher relative to control. Soil microbial analysis showed that mycorrhizal spore counts in BB-amended soils were 133% (Liliw), 262% (Magdalena) and 109% (Lipa) higher than the control. Nitrogen-fixing bacteria obtained from MR + BB-amended soils in Liliw were 216% higher than control, and 81% higher relative to control in BB-treated soils in Lipa. Soil nitrogen and potassium contents of the three cacao farms also improved by 26-85%. With the significant effect of bamboo biochar and mycorrhizal fertilizer, alone or in combination, on the growth of cacao, the microbial community and nutrient status of the cacao rhizosphere soil, this technology would be beneficial to cacao farmers and to almost all crops in an agroforest ecosystem.
Assessing Willingness to Pay for Improved Water Services from Forest Area in Bayas Jaya Village, Lampung Province
Authors: Abidin Z. , Efendi I. , Gultom D.T. 
Published: February 2023

Abstract
One of the important functions of the forest is to provide water to the community. Improvement of water services from forest areas requires the community’s participation. This study aims at (1) identifying the community’s willingness to pay for improved water services and (2) determining factors affecting the community’s willingness to pay. This study is located in Bayas Jaya Villages and the upland area of Kedondong Sub-District, Pesawaran District, Lampung Province. The study interviewed 75 farmers of 3 water services management, i.e.: (1) independent, (2) PAMSIMAS, and (3) PDAM. Each management water service was represented by 25 members who were randomly selected. Objective one is analyzed using descriptive analysis, and objective two is analyzed using a regression analysis model. The study suggests that, on average community received 10,6m3 per day, which is far higher than their daily consumed, i.e., 460 l per day. However, water surplus is not optimized as they are drained to the local sewer. Further, 56% of the community is willing to pay should water services be improved. The average willingness to pay is Rp 440,357.14 annually per family. Factors affecting the community’s willingness to pay, include (1) the PDAM model, (2) the PAMSIMAS model, (3) age, and (4) daily water discharge to family.
In planta evidence that the HAK transporter OsHAK2 is involved in Na+ transport in rice
Authors: Morita Shigeto , Tamba Natsumi , Shibasaka Mineo , Sasano Shizuka , Kadoike Taiju , Urase Yasuyo , Maruyama Masamitsu , Fukuoka Aguri , Yanai Junta , Masumura Takehiro , Ogihara Yasunari , Satoh Shigeru , Tanaka Kunisuke , Katsuhara Maki , Nakayama Hideki 
Published: February 2023

ABSTRACT
HAK family transporters primarily function as K+ transporters and play major roles in K+ uptake and translocation in plants, whereas several HAK transporters exhibit Na+ transport activity. OsHAK2, a rice HAK transporter, was shown to mediate Na+ transport in Escherichia coli in a previous study. In this study, we investigated whether OsHAK2 is involved in Na+ transport in the rice plant. Overexpression of OsHAK2 increased Na+ translocation from the roots to the shoots of transgenic rice. It also increased both root and whole-plant Na+ content, and enhanced shoot length under low Na+ and K+ conditions. Meanwhile, OsHAK2 overexpression increased salt sensitivity under a long-term salt stress condition, indicating that OsHAK2 is not involved in salt tolerance, unlike in the case of ZmHAK4 in maize. These results suggest that OsHAK2 is permeable to Na+ and contributes to shoot growth in rice plants under low Na+ and K+ conditions.
Identification of genes responsible for absorbing palladium ion in Escherichia coli
Authors: Matsumoto Takuya , Tanaka Yoshitaka , Kamino Mizuho , Yamada Ryosuke , Konishi Yasuhiro , Ogino Hiroyasu 
Published: February 2023

ABSTRACT
The capability of Escherichia coli BW25113 to adsorb palladium (Pd) ions in a single-gene-knockout library was investigated using high-throughput screening. The results revealed that compared to BW25113, nine strains promoted Pd ion adsorption, whereas 22 strains repressed. Although further studies are required because of the first screening results, our results will provide a new perspective for improving the biosorption.
Comparison of long- and short-read metagenomic assembly for low-abundance species and resistance genes
Authors: Yorki Sosie , Shea Terrance , Cuomo Christina A , Walker Bruce J , LaRocque Regina C , Manson Abigail L , Earl Ashlee M , Worby Colin J 
Published: February 2023

AbstractRecent technological and computational advances have made metagenomic assembly a viable approach to achieving high-resolution views of complex microbial communities. In previous benchmarking, short-read (SR) metagenomic assemblers had the highest accuracy, long-read (LR) assemblers generated the most contiguous sequences and hybrid (HY) assemblers balanced length and accuracy. However, no assessments have specifically compared the performance of these assemblers on low-abundance species, which include clinically relevant organisms in the gut. We generated semi-synthetic LR and SR datasets by spiking small and increasing amounts of Escherichia coli isolate reads into fecal metagenomes and, using different assemblers, examined E. coli contigs and the presence of antibiotic resistance genes (ARGs). For ARG assembly, although SR assemblers recovered more ARGs with high accuracy, even at low coverages, LR assemblies allowed for the placement of ARGs within longer, E. coli-specific contigs, thus pinpointing their taxonomic origin. HY assemblies identified resistance genes with high accuracy and had lower contiguity than LR assemblies. Each assembler type’s strengths were maintained even when our isolate was spiked in with a competing strain, which fragmented and reduced the accuracy of all assemblies. For strain characterization and determining gene context, LR assembly is optimal, while for base-accurate gene identification, SR assemblers outperform other options. HY assembly offers contiguity and base accuracy, but requires generating data on multiple platforms, and may suffer high misassembly rates when strain diversity exists. Our results highlight the trade-offs associated with each approach for recovering low-abundance taxa, and that the optimal approach is goal-dependent.
The repertoire of copy number alteration signatures in human cancer
Authors: Tao Ziyu , Wang Shixiang , Wu Chenxu , Wu Tao , Zhao Xiangyu , Ning Wei , Wang Guangshuai , Wang Jinyu , Chen Jing , Diao Kaixuan , Chen Fuxiang , Liu Xue-Song 
Published: February 2023

AbstractCopy number alterations (CNAs) are a predominant source of genetic alterations in human cancer and play an important role in cancer progression. However comprehensive understanding of the mutational processes and signatures of CNA is still lacking. Here we developed a mechanism-agnostic method to categorize CNA based on various fragment properties, which reflect the consequences of mutagenic processes and can be extracted from different types of data, including whole genome sequencing (WGS) and single nucleotide polymorphism (SNP) array. The 14 signatures of CNA have been extracted from 2778 pan-cancer analysis of whole genomes WGS samples, and further validated with 10 851 the cancer genome atlas SNP array dataset. Novel patterns of CNA have been revealed through this study. The activities of some CNA signatures consistently predict cancer patients’ prognosis. This study provides a repertoire for understanding the signatures of CNA in cancer, with potential implications for cancer prognosis, evolution and etiology.
Antireflux surgery versus medical management of gastro-oesophageal reflux after lung transplantation
Authors: Razia Deepika , Mittal Sumeet K , Fournier Sarah , Walia Rajat , Smith Michael A , Bremner Ross M , Huang Jasmine L 
Published: February 2023

AbstractOBJECTIVESGastro-oesophageal reflux disease after lung transplantation may be associated with chronic lung allograft dysfunction. Aspiration may continue on medical management of reflux, but antireflux surgery potentially reduces all reflux. We compared outcomes between medical and surgical management of reflux in lung recipients.METHODSLung recipients with an elevated DeMeester score (≥14.72) on post-transplant reflux testing between 2015 and 2020 were included. Patients were divided into 2 groups: group A (underwent surgery) and group B (medically managed). Endpoints were pulmonary function, allograft dysfunction-free survival and overall survival. Further analysis included subgroups: A1 (early surgery, &lt;6 months) and A2 (late surgery, &gt;6 months), and B1 (DeMeester &lt;29.9) and B2 (DeMeester ≥30).RESULTSA total of 186 included subjects were divided into groups A [n = 46 (A1, n = 36; A2, n = 10)] and B [n = 140 (B1, n = 78; B2, n = 62)]. Compared to medically managed patients, patients who underwent surgery had a higher prevalence of hiatal hernia (P &lt; 0.001) and a lower prevalence of oesophageal motility disorders (P = 0.036). Recipients who underwent surgery had superior pulmonary function at 5 years compared to group B (P &lt; 0.05) and longer allograft dysfunction-free survival than subgroup B2 (P = 0.028). Furthermore, early surgery was associated with longer survival than late surgery (P = 0.021).CONCLUSIONSAntireflux surgery in recipients with reflux improved long-term allograft function, and early surgery showed a survival benefit. Allograft dysfunction-free survival of lung recipients who underwent surgery was significantly better than that of medically managed patients with DeMeester ≥30. We present an algorithm for appropriate selection of candidates for antireflux surgery after lung transplantation.
Impractical Criticism
Authors: Jones Ewan 
Published: February 2023

Abstract
On 25 October 2017, the Daily Telegraph falsely accused an undergraduate student of demanding that the University of Cambridge ‘drop male authors’. This essay takes the polemics around this episode as jumping-off point for a wider discussion of pedagogical method. It argues that the defamiliarizing procedures of practical criticism, which have been the subject of much ideological critique, can be extended and amended in a manner that reveals implicit bias, re-habituates cognitive routine, and restores the body to critical response. It concludes with one instance of such pedagogical method.
Genome assembly of Musa beccarii shows extensive chromosomal rearrangements and genome expansion during evolution of Musaceae genomes
Authors: Wang Zheng-Feng , Rouard Mathieu , Droc Gaetan , Heslop-Harrison Pat (J S) , Ge Xue-Jun 
Published: February 2023

Abstract

Background
Musa beccarii (Musaceae) is a banana species native to Borneo, sometimes grown as an ornamental plant. The basic chromosome number of Musa species is x = 7, 10, or 11; however, M. beccarii has a basic chromosome number of x = 9 (2n = 2x = 18), which is the same basic chromosome number of species in the sister genera Ensete and Musella. Musa beccarii is in the section Callimusa, which is sister to the section Musa. We generated a high-quality chromosome-scale genome assembly of M. beccarii to better understand the evolution and diversity of genomes within the family Musaceae.

Findings
The M. beccarii genome was assembled by long-read and Hi-C sequencing, and genes were annotated using both long Iso-seq and short RNA-seq reads. The size of M. beccarii was the largest among all known Musaceae assemblies (∼570 Mbp) due to the expansion of transposable elements and increased 45S ribosomal DNA sites. By synteny analysis, we detected extensive genome-wide chromosome fusions and fissions between M. beccarii and the other Musa and Ensete species, far beyond those expected from differences in chromosome number. Within Musaceae, M. beccarii showed a reduced number of terpenoid synthase genes, which are related to chemical defense, and enrichment in lipid metabolism genes linked to the physical defense of the cell wall. Furthermore, type III polyketide synthase was the most abundant biosynthetic gene cluster (BGC) in M. beccarii. BGCs were not conserved in Musaceae genomes.

Conclusions
The genome assembly of M. beccarii is the first chromosome-scale genome assembly in the Callimusa section in Musa, which provides an important genetic resource that aids our understanding of the evolution of Musaceae genomes and enhances our knowledge of the pangenome.
Maximum norm a posteriori error estimates for convection–diffusion problems
Authors: Demlow Alan , Franz Sebastian , Kopteva Natalia 
Published: February 2023

Abstract
We prove residual-type a posteriori error estimates in the maximum norm for a linear scalar elliptic convection–diffusion problem that may be singularly perturbed. Similar error analysis in the energy norm by Verfürth indicates that a dual norm of the convective derivative of the error must be added to the natural energy norm in order for the natural residual estimator to be reliable and efficient. We show that the situation is similar for the maximum norm. In particular, we define a mesh-dependent weighted seminorm of the convective error, which functions as a maximum-norm counterpart to the dual norm used in the energy norm setting. The total error is then defined as the sum of this seminorm, the maximum norm of the error and data oscillation. The natural maximum norm residual error estimator is shown to be equivalent to this total error notion, with constant independent of singular perturbation parameters. These estimates are proved under the assumption that certain natural estimates hold for the Green’s function for the problem at hand. Numerical experiments confirm that our estimators effectively capture the maximum-norm error behavior for singularly perturbed problems, and can effectively drive adaptive refinement in order to capture layer phenomena.
A Mixing Property for the Action of SL(3,ℤ) × SL(3,ℤ) on the Stone–Čech Boundary of SL(3,ℤ)
Authors: Bassi J , Rădulescu F 
Published: February 2023

Abstract
By analogy with the construction of the Furstenberg boundary, the Stone–Čech boundary of $\textrm {SL}(3,\mathbb {Z})$ is a fibered space over products of projective matrices. The proximal behaviour on this space is exploited to show that the preimages of certain sequences have accumulation points that belong to specific regions, defined in terms of flags. We show that the $\textrm {SL}(3,\mathbb {Z})\times \textrm {SL}(3,\mathbb {Z})$-quasi-invariant Radon measures supported on these regions are tempered. Thus, every quasi-invariant Radon boundary measure for $\textrm {SL}(3,\mathbb {Z})$ is an orthogonal sum of a tempered measure and a measure having matrix coefficients belonging to a certain ideal $c^{\prime}_0 ((\textrm {SL}(3,\mathbb {Z}) \times \textrm {SL}(3,\mathbb {Z}))$, slightly larger than $c_0 ((\textrm {SL}(3,\mathbb {Z}) \times \textrm {SL}(3,\mathbb {Z}))$. Hence, the left–right representation of $C^*(\textrm {SL}(3,\mathbb {Z}) \times \textrm {SL}(3,\mathbb {Z}))$ in the Calkin algebra of $\textrm {SL}(3,\mathbb {Z})$ factors through $C^*_{c^{\prime}_0} (\textrm {SL}(3,\mathbb {Z}) \times \textrm {SL}(3,\mathbb {Z}))$ and the centralizer of every infinite subgroup of $\textrm {SL}(3,\mathbb {Z})$ is amenable.
Curved Versions of the Ovsienko–Redou Operators
Authors: Case Jeffrey S , Lin Yueh-Ju , Yuan Wei 
Published: February 2023

Abstract
We construct a family of conformally covariant bidifferential operators on pseudo-Riemannian manifolds. Our construction is analogous to the construction of Graham–Jenne–Mason–Sparling of conformally covariant differential operators via tangential powers of the Laplacian in the Fefferman–Graham ambient space. In fact, we completely classify the tangential bidifferential operators on the ambient space, which are expressed purely in terms of the ambient Laplacian. This gives a curved analogue of the classification, due to Ovsienko–Redou and Clerc, of conformally invariant bidifferential operators on the sphere. As an application, we construct a large class of formally self-adjoint conformally invariant differential operators.
Managing re-identification risks while providing access to the All of Us research program
Authors: Xia Weiyi , Basford Melissa , Carroll Robert , Clayton Ellen Wright , Harris Paul , Kantacioglu Murat , Liu Yongtai , Nyemba Steve , Vorobeychik Yevgeniy , Wan Zhiyu , Malin Bradley A 
Published: February 2023

Abstract

Objective
The All of Us Research Program makes individual-level data available to researchers while protecting the participants’ privacy. This article describes the protections embedded in the multistep access process, with a particular focus on how the data was transformed to meet generally accepted re-identification risk levels.

Methods
At the time of the study, the resource consisted of 329 084 participants. Systematic amendments were applied to the data to mitigate re-identification risk (eg, generalization of geographic regions, suppression of public events, and randomization of dates). We computed the re-identification risk for each participant using a state-of-the-art adversarial model specifically assuming that it is known that someone is a participant in the program. We confirmed the expected risk is no greater than 0.09, a threshold that is consistent with guidelines from various US state and federal agencies. We further investigated how risk varied as a function of participant demographics.

Results
The results indicated that 95th percentile of the re-identification risk of all the participants is below current thresholds. At the same time, we observed that risk levels were higher for certain race, ethnic, and genders.

Conclusions
While the re-identification risk was sufficiently low, this does not imply that the system is devoid of risk. Rather, All of Us uses a multipronged data protection strategy that includes strong authentication practices, active monitoring of data misuse, and penalization mechanisms for users who violate terms of service.
Analysis of runs of homozygosity of cattle living in different climate zones
Authors: Falchi Laura , Cesarani Alberto , Mastrangelo Salvatore , Senczuk Gabriele , Portolano Baldassare , Pilla Fabio , Macciotta Nicolò P P 
Published: February 2023

AbstractAim of this study was to analyze the distribution and characteristics of runs of homozygosity in Bos taurus taurus and Bos taurus indicus breeds, as well as their crosses, farmed all around the world. With this aim in view, we used single-nucleotide polymorphisms (SNP) genotypes for 3,263 cattle belonging to 204 different breeds. After quality control, 23,311 SNPs were retained for the analysis. Animals were divided into seven different groups: 1) continental taurus, 2) temperate taurus, 3) temperate indicus, 4) temperate composite, 5) tropical taurus, 6) tropical indicus, and 7) tropical composite. The climatic zones were created according to the latitude of the breeds’ country of origin: i) continental, latitude ≥ 45°; ii) temperate, 45°&lt; Latitude &gt;23.26°; iii) tropics, latitude ≤ 23.26°. Runs of homozygosity were computed as 15 SNPs spanning in at least 2 Mb; number of ROH per animal (nROH), average ROH length (meanMb), and ROH-based inbreeding coefficients (FROH) were also computed. Temperate indicus showed the largest nROH, whereas Temperate taurus the lowest value. Moreover, the largest meanMb was observed for Temperate taurus, whereas the lowest value for Tropics indicus. Temperate indicus breeds showed the largest FROH values. Genes mapped in the identified ROH were reported to be associated with the environmental adaptation, disease resistance, coat color determinism, and production traits. Results of the present study confirmed that runs of homozygosity could be used to identify genomic signatures due to both artificial and natural selection.
Prevalence of Suicide by Self-immolation Among Children in Southern Iran
Authors: Shahriarirad Reza , Ranjbar Keivan , Erfani Amirhossein , Modarresi Mahboobeh-Sadat , Koranishiraz Amirhossein , Kamali Morvarid , Zardosht Mitra , Mohammadi Ali Akbar 
Published: February 2023

Abstract
Self-immolation is considered among the most rigorous acts of suicide. Lately, this act has increased in children. We evaluated the frequency of self-immolation among children in the largest burn referral center in southern Iran. This cross-sectional study was conducted from January 2014 to the end of 2018 at a tertiary referral burn and plastic surgery healthcare center in southern Iran. Subjects were pediatric self-immolation burn patients registered as outpatients or inpatients. The patients’ parents were contacted regarding any incomplete information. Among 913 children admitted due to burn injuries, 14 (1.55%) were admitted with an impression of suicidal self-immolation. Among self-immolation patients, the ages ranged from 11 to 15 years (mean: 13.64 ± 1.33), and the average burnt percentage of total body surface area was 67.07 ± 31.19%. The male-to-female ratio was 1:1, and the majority were from urban areas (57.1%). The most frequent cause of burn injury was fire (92.9%). There was no history of family mental illness or suicide among the patients, and only one of the patients had an underlying disease of intellectual disability. The mortality percentage was 64.3%. The percentage of childhood suicidal attempts by burn injuries was alarmingly high among children aged from 11 to 15. While contrary to many reports, we reported this phenomenon to be relatively similar between genders, and also between urban and rural patients. Compared with accidental burn injuries, the self-immolation group had significantly higher age and burn percentage, and were more frequently caused by fire, occurred outdoors, and resulted in mortality.