bluuebunny/crossref_metadata_2025_split huggingface dataset:
Descending from A to B along the quickest path
Authors: Cross Rod 
Published: July 2022

Abstract
A simple experiment is described to compare the descent time between two vertically separated points when an object slides down tracks of varying shape. A surprising result is that the descent time is shortest when it follows a circular track rather than a cycloidal track. Cycloidal tracks are usually predicted to result in the shortest descent time, but only if friction is negligible.
A multi-layer strip ionization chamber (MLSIC) device for proton pencil beam scan quality assurance
Authors: Zhou Shuang , Rao Wei , Chen Qinghao , Tan Yuewen , Smith Winter , Sun Baozhou , Zhou Jun , Chang Chih-Wei , Lin Liyong , Darafsheh Arash , Zhao Tianyu , Zhang Tiezhi 
Published: July 2022

Abstract

Objective. Proton pencil beam scanning (PBS) treatment fields needs to be verified before treatment deliveries to ensure patient safety. In current practice, treatment beam quality assurance (QA) is measured at a few selected depths using film or a 2D detector array, which is insensitive and time-consuming. A QA device that can measure all key dosimetric characteristics of treatment beams spot-by-spot within a single beam delivery is highly desired. Approach. We developed a multi-layer strip ionization chamber (MLSIC) prototype device that comprises of two layers of strip ionization chambers (IC) plates for spot position measurement and 64 layers of plate IC for beam energy measurement. The 768-channel strip ion chamber signals are integrated and sampled at a speed of 3.125 kHz. It has a 25.6 cm × 25.6 cm maximum measurement field size and 2 mm spatial resolution for spot position measurement. The depth resolution and maximum depth were 2.91 mm and 18.6 cm for 1.6 mm thick IC plate, respectively. The relative weight of each spot was determined from total charge by all IC detector channels. Main results. The MLSIC is able to measure ionization currents spot-by-spot. The depth dose measurement has a good agreement with the ground truth measured using a water tank and commercial one-dimensional (1D) multi-layer plate chamber. It can verify the spot position, energy, and relative weight of clinical PBS beams and compared with the treatment plans. Significance. The MLSIC is a highly efficient QA device that can measure the key dosimetric characteristics of proton treatment beams spot-by-spot with a single beam delivery. It may improve the quality and efficiency of clinical proton treatments.
Neutron-induced nuclear recoil background in the PandaX-4T experiment*
Authors: Huang Zhou , Shen Guofang , Wang Qiuhong , Abdukerim Abdusalam , Bo Zihao , Chen Wei , Chen Xun , Chen Yunhua , Cheng Chen , Cheng Yunshan , Cui Xiangyi , Fan Yingjie , Fang Deqing , Fu Changbo , Fu Mengting , Geng Lisheng , Giboni Karl , Gu Linhui , Guo Xuyuan , Han Chencheng , Han Ke , He Changda , He Jinrong , Huang Di , Huang Yanlin , Hou Ruquan , Ji Xiangdong , Ju Yonglin , Li Chenxiang , Li Mingchuan , Li Shu , Li Shuaijie , Lin Qing , Liu Jianglai , Lu Xiaoying , Luo Lingyin , Ma Wenbo , Ma Yugang , Mao Yajun , Meng Yue , Ning Xuyang , Qi Ningchun , Qian Zhicheng , Ren Xiangxiang , Shaheed Nasir , Shang Changsong , Si Lin , Sun Wenliang , Tan Andi , Tao Yi , Wang Anqing , Wang Meng , Wang Shaobo , Wang Siguang , Wang Wei , Wang Xiuli , Wang Zhou , Wu Mengmeng , Wu Weihao , Xia Jingkai , Xiao Mengjiao , Xiao Xiang , Xie Pengwei , Yan Binbin , Yan Xiyu , Yang Jijun , Yang Yong , Yu Chunxu , Yuan Jumin , Yuan Ying , Zhang Dan , Zhang Minzhen , Zhang Peng , Zhang Tao , Zhao Li , Zheng Qibin , Zhou Jifang , Zhou Ning , Zhou Xiaopeng , Zhou Yong 
Published: July 2022

Abstract
Neutron-induced nuclear recoil background is critical to dark matter searches in the PandaX-4T liquid xenon experiment. In this study, we investigate the features of neutron background in liquid xenon and evaluate its contribution in single scattering nuclear recoil events using three methods. The first method is fully based on Monte Carlo simulations. The last two are data-driven methods that also use multiple scattering signals and high energy signals in the data. In the PandaX-4T commissioning data with an exposure of 0.63 tonne-year, all these methods give a consistent result, i.e., there are

neutron-induced backgrounds in the dark matter signal region within an approximated nuclear recoil energy window between 5 and 100 keV.
Future population transgress climatic risk boundaries of extreme temperature and precipitation
Authors: Sano Taichi , Oki Taikan 
Published: July 2022

Abstract
Anthropogenic climate change is influencing the frequencies of extreme weather events. Considering the adaptability to extreme climatic risks in the future, we focused on determining whether humans have been exposed to the risks before. We define the rim of two-dimensional histograms of population under 20-year extreme temperature and precipitation as a climatic risk boundary. More than 30% (16.3%) of world population in South Asia, sub-Saharan Africa, and other regions will transgress the climatic risk boundary by the end of this century under RCP8.5 (RCP2.6) scenario. While many areas with large cities will remain within the global climatic risk boundary, they will transgress their regional climatic risk boundaries. This study shows that it is also necessary to consider the limits to adaptation for each appropriate area, considering the cultural, technological, and social transferability of adaptation. This study will help refine public perceptions of extreme climatic risks and lead to more efficient policy making.
Suppression of charge-density-wave order in TiSe2 studied with high-pressure magnetoresistance
Authors: Moulding Owen , Muramatsu Takaki , Sayers Charles J , Da Como Enrico , Friedemann Sven 
Published: July 2022

Abstract
TiSe2 undergoes charge density wave (CDW) order which can be suppressed under pressure. We use high-resolution electrical resistivity and magnetoresistance measurements to trace the CDW to the highest pressures of any transport study so far. Comparison with previous work shows that the CDW is very sensitive to pressure conditions resulting in a reduced critical pressure in the presence of non-hydrostaticity. Our analysis indicates that in perfect pressure conditions the intrinsic critical pressure might be as high as 5.6 GPa. At the same time, we observe signatures of enhanced scattering linked to the critical pressure, P
CDW. The sensitivity of P
CDW to non-hydrostaticity and the enhanced scattering linked to it raises questions of how the superconductivity induced in TiSe2 under pressure is related to the CDW order.
Differences Between Semantic and Phonemic Verbal Fluency in Adolescents With Reading Disorders
Authors: Kavé Gitit , Sapir-Yogev Smadar 
Published: July 2022

Abstract

Objectives
This study aimed to examine which verbal fluency task is most useful in assessing adolescents with reading disorders (RD).

Method
Eighty-three Hebrew-speaking adolescents (ages 12–15), 42 of them with RD, completed semantic and phonemic fluency tasks, and their scores were converted to standardized scores according to population norms.

Results
Scores on the semantic task were similar in the RD and the control group, unlike scores on the phonemic task, which were significantly lower in the RD group. The RD group demonstrated higher semantic than phonemic scores, unlike the control group whose standardized scores on both tasks were similar. Phonemic but not semantic fluency scores predicted spelling scores within the RD group.

Conclusions
Adolescents with RD have no difficulty on a semantic fluency task, but perform below expected age-matched levels on the phonemic fluency task. To document this task-difference, practitioners must administer both fluency tasks when assessing RD.
The K-mer File Format: a standardized and compact disk representation of sets ofk-mers
Authors: Dufresne Yoann , Lemane Teo , Marijon Pierre , Peterlongo Pierre , Rahman Amatur , Kokot Marek , Medvedev Paul , Deorowicz Sebastian , Chikhi Rayan 
Published: July 2022

AbstractSummaryBioinformatics applications increasingly rely on ad hoc disk storage of k-mer sets, e.g. for de Bruijn graphs or alignment indexes. Here, we introduce the K-mer File Format as a general lossless framework for storing and manipulating k-mer sets, realizing space savings of 3–5× compared to other formats, and bringing interoperability across tools.Availability and implementationFormat specification, C++/Rust API, tools: https://github.com/Kmer-File-Format/.Supplementary informationSupplementary data are available at Bioinformatics online.
Antivirals With Activity Against Mpox: A Clinically Oriented Review
Authors: Siegrist Emily A , Sassine Joseph 
Published: July 2022

Abstract
Mpox virus is an emergent human pathogen. While it is less lethal than smallpox, it can still cause significant morbidity and mortality. In this review, we explore 3 antiviral agents with activity against mpox and other orthopoxviruses: cidofovir, brincidofovir, and tecovirimat. Cidofovir, and its prodrug brincidofovir, are inhibitors of DNA replication with a broad spectrum of activity against multiple families of double-stranded DNA viruses. Tecovirimat has more specific activity against orthopoxviruses and inhibits the formation of the extracellular enveloped virus necessary for cell-to-cell transmission. For each agent, we review basic pharmacology, data from animal models, and reported experience in human patients.
Size at Birth, Postnatal Growth, and Reproductive Timing in an Australian Microbat
Authors: Eastick D L , Griffiths S R , Yen J D L , Robert K A 
Published: July 2022

SynopsisReproductive phenology, size at birth, and postnatal growth are important life history traits that reflect parental investment. The ability to document detailed changes in these traits can be a valuable tool in the identification and management of at-risk wildlife populations. We examined reproductive traits in a common, widespread Australian microbat, Chalinolobus gouldii, at two sites over two years and derived growth curves and age estimation equations which will be useful in the study of how intrinsic and extrinsic factors alter parental investment strategies. We found that male and female offspring did not differ significantly in their size at birth or their postnatal growth rates. Bats born in 2018 were smaller at birth but grew at a faster rate than those born in 2017. When date of birth was compared across sites and years, we found bats born in 2018 had a later median birthdate (by 18 days) and births were more widespread than those born in 2017. Cooler and wetter weather during late gestation (Nov) in 2018 may have prolonged gestation and delayed births. With many bats facing threatening processes it is important to study reproductive plasticity in common and widespread “model” species, which may assist in the conservation and management of threatened microbats with similar reproductive traits.
Comparing “people-like-me” and linear mixed model predictions of functional recovery following knee arthroplasty
Authors: Graber Jeremy , Kittelson Andrew , Juarez-Colunga Elizabeth , Jin Xin , Bade Michael , Stevens-Lapsley Jennifer 
Published: July 2022

Abstract

Objective
Prediction models can be useful tools for monitoring patient status and personalizing treatment in health care. The goal of this study was to compare the relative strengths and weaknesses of 2 different approaches for predicting functional recovery after knee arthroplasty: a neighbors-based “people-like-me” (PLM) approach and a linear mixed model (LMM) approach.

Materials and Methods
We used 2 distinct datasets to train and then test PLM and LMM prediction approaches for functional recovery following knee arthroplasty. We used the Timed Up and Go (TUG)—a common test of mobility—to operationalize physical function. Both approaches used patient characteristics and baseline postoperative TUG values to predict TUG recovery from days 1–425 following surgery. We then compared the accuracy and precision of PLM and LMM predictions.

Results
A total of 317 patient records with 1379 TUG observations were used to train PLM and LMM approaches, and 456 patient records with 1244 TUG observations were used to test the predictions. The approaches performed similarly in terms of mean squared error and bias, but the PLM approach provided more accurate and precise estimates of prediction uncertainty.

Discussion and Conclusion
Overall, the PLM approach more accurately and precisely predicted TUG recovery following knee arthroplasty. These results suggest PLM predictions may be more clinically useful for monitoring recovery and personalizing care following knee arthroplasty. However, clinicians and organizations seeking to use predictions in practice should consider additional factors (eg, resource requirements) when selecting a prediction approach.
Travel-associated extensively drug-resistant typhoid fever: a case series to inform management in non-endemic regions
Authors: Posen H Joshua , Wong Waison , Farrar Daniel S , Campigotto Aaron , Chan Tiffany , Barker Kevin R , Hagmann Stefan H F , Ryan Edward T , LaRocque Regina C , Earl Ashlee M , Worby Colin J , Castelli Francesco , Fumadó Victoria Pérez , Britton Philip N , Libman Michael , Hamer Davidson H , Morris Shaun K 
Published: July 2022

AbstractBackgroundExtensively drug-resistant (XDR) typhoid fever is a threat to travelers to Pakistan. We describe a multicontinental case series of travel-acquired XDR typhoid fever to demonstrate the global spread of the problem and encourage preventive interventions as well as appropriate empiric antimicrobial use.MethodsCases were extracted from the GeoSentinel database, microbiologic laboratory records of two large hospitals in Toronto, Canada, and by invitation to TropNet sites. All isolates were confirmed XDR Salmonella enterica serovar Typhi (Salmonella typhi), with resistance to ampicillin, ceftriaxone, ciprofloxacin and trimethoprim–sulfamethoxazole.ResultsSeventeen cases were identified in Canada (10), USA (2), Spain (2), Italy (1), Australia (1) and Norway (1). Patients under 18 years represented 71% (12/17) of cases, and all patients travelled to Pakistan to visit friends or relatives. Only one patient is known to have been vaccinated. Predominant symptoms were fever, abdominal pain, vomiting and diarrhoea. Antimicrobial therapy was started on Day 1 of presentation in 75% (12/16) of patients, and transition to a carbapenem or azithromycin occurred a median of 2 days after blood culture was drawn. Antimicrobial susceptibilities were consistent with the XDR S. typhi phenotype, and whole genome sequencing on three isolates confirmed their belonging to the XDR variant of the H58 clade.ConclusionsXDR typhoid fever is a particular risk for travelers to Pakistan, and empiric use of a carbapenem or azithromycin should be considered. Pre-travel typhoid vaccination and counseling are necessary and urgent interventions, especially for visiting friends and relatives travelers. Ongoing sentinel surveillance of XDR typhoid fever is needed to understand changing epidemiology.
The dichotomy between low-frequency-peaked BL Lacs and flat-spectrum radio quasars
Authors: Cheng Y P , Kang S J , Zheng Y G 
Published: July 2022

ABSTRACT
By comparing the Fourth Fermi Large Area Telescope active galactic nuclei (AGNs) Catalog Data Release 2 (4LAC-DR2) and the Radio Fundamental Catalog (RFC-2021b), we obtain an AGN sample containing 2816 AGNs. We calculate the γ-ray loudness (Gγ) of the sample sources, and establish the relevant relationship between several gamma/radio properties. The results show that: 1) the synchrotron peak frequency ($\nu _\mathrm{peak}^S$) strongly correlates with the γ-ray photon spectral index (Γγ), γ-ray luminosity (Lγ), and radio luminosity (LR); 2) the low-synchrotron-peaked BL Lac objects (LBLs) and the flat-spectrum radio quasars (FSRQs) partially overlap in log $\nu _\mathrm{peak}^S\!-\!\Gamma _\gamma$, log Lγ–Γγ, log LR–Γγ, log Gγ–Γγ, log $\nu _\mathrm{peak}^S\!-\!$log Lγ, log $\nu _\mathrm{peak}^S\!-\!$log LR, and log $\nu _\mathrm{peak}^S\!-\!$log Gγ space. We plotted the distribution of redshift (z), $\nu _\mathrm{peak}^S$, Γγ, Lγ, VLBI 8.4 GHz flux density ($S_{\rm {8.4\, GHz}}$), and Gγ to distinguish FSRQs and LBLs. We note that $\nu _\mathrm{peak}^S$, Γγ, and $S_{8.4\, {\rm GHz}}$ show similar bimodal distributions. To further determine whether FSRQs are misjudged as LBLs, we examined the Compton dominance (CD), and found that CD &lt; 1 for only two out of 39 sources. This measurement provides further evidence that FSRQs may be mistaken for LBLs.
Impact of H2-driven star formation and stellar feedback from low-enrichment environments on the formation of spiral galaxies
Authors: Valentini Milena , Dolag Klaus , Borgani Stefano , Murante Giuseppe , Maio Umberto , Tornatore Luca , Granato Gian Luigi , Ragone-Figueroa Cinthia , Burkert Andreas , Ragagnin Antonio , Rasia Elena 
Published: July 2022

ABSTRACT
The reservoir of molecular gas (H2) represents the fuel for the star formation (SF) of a galaxy. Connecting the star formation rate (SFR) to the available H2 is key to accurately model SF in cosmological simulations of galaxy formation. We investigate how modifying the underlying modelling of H2 and the description of stellar feedback in low-metallicity environments (LMF, i.e. low-metallicity stellar feedback) in cosmological zoomed-in simulations of a Milky Way-size halo influences the formation history of the forming, spiral galaxy, and its final properties. We exploit two different models to compute the molecular fraction of cold gas ($f_{\rm H_{2}}$): (i) the theoretical model by Krumholz et al. (2009b) and (ii) the phenomenological prescription by Blitz and Rosolowsky (2006). We find that the model adopted to estimate $f_{\rm H_{2}}$ plays a key role in determining final properties and in shaping the morphology of the galaxy. The clumpier interstellar medium (ISM) and the more complex H2 distribution that the Krumholz et al. model predicts result in better agreement with observations of nearby disc galaxies. This shows how crucial it is to link the SFR to the physical properties of the star-forming, molecular ISM. The additional source of energy that LMF supplies in a metal-poor ISM is key in controlling SF at high redshift and in regulating the reservoir of SF across cosmic time. Not only is LMF able to regulate cooling properties of the ISM, but it also reduces the stellar mass of the galaxy bulge. These findings can foster the improvement of the numerical modelling of SF in cosmological simulations.
The bluetides mock image catalogue: simulated observations of high-redshift galaxies and predictions for JWST imaging surveys
Authors: Marshall Madeline A , Watts Katelyn , Wilkins Stephen , Matteo Tiziana Di , Kuusisto Jussi K , Roper William J , Vijayan Aswin P , Ni Yueying , Feng Yu , Croft Rupert A C 
Published: July 2022

ABSTRACT
We present a mock image catalogue of ∼100 000 MUV ≃ −22.5 to −19.6 mag galaxies at z = 7–12 from the bluetides cosmological simulation. We create mock images of each galaxy with the James Webb Space Telescope (JWST), Hubble, Roman, and Euclid Space Telescopes, as well as Subaru, and VISTA, with a range of near- and mid-infrared filters. We perform photometry on the mock images to estimate the success of these instruments for detecting high-z galaxies. We predict that JWST will have unprecedented power in detecting high-z galaxies, with a 95 per cent completeness limit at least 2.5 mag fainter than VISTA and Subaru, 1.1 mag fainter than Hubble, and 0.9 mag fainter than Roman, for the same wavelength and exposure time. Focusing on JWST, we consider a range of exposure times and filters, and find that the NIRCam F356W and F277W filters will detect the faintest galaxies, with 95 per cent completeness at m ≃ 27.4 mag in 10-ks exposures. We also predict the number of high-z galaxies that will be discovered by upcoming JWST imaging surveys. We predict that the COSMOS-Web survey will detect ∼1000 M1500 Å &lt; −20.1 mag galaxies at 6.5 &lt; z &lt; 7.5, by virtue of its large survey area. JADES-Medium will detect almost $100{{\ \rm per\ cent}}$ of M1500 Å ≲ −20 mag galaxies at z &lt; 8.5 due to its significant depth, however, with its smaller survey area it will detect only ∼100 of these galaxies at 6.5 &lt; z &lt; 7.5. Cosmic variance results in a large range in the number of predicted galaxies each survey will detect, which is more evident in smaller surveys such as CEERS and the PEARLS NEP and GOODS-S fields.
Repeat Dynamics across Timescales: A Perspective from Sibling Allotetraploid Marsh Orchids (Dactylorhiza majaliss.l.)
Authors: Eriksson Mimmi C , Mandáková Terezie , McCann Jamie , Temsch Eva M , Chase Mark W , Hedrén Mikael , Weiss-Schneeweiss Hanna , Paun Ovidiu 
Published: July 2022

AbstractTo provide insights into the fate of transposable elements (TEs) across timescales in a post-polyploidization context, we comparatively investigate five sibling Dactylorhiza allotetraploids (Orchidaceae) formed independently and sequentially between 500 and 100K generations ago by unidirectional hybridization between diploids D. fuchsii and D. incarnata. Our results first reveal that the paternal D. incarnata genome shows a marked increased content of LTR retrotransposons compared to the maternal species, reflected in its larger genome size and consistent with a previously hypothesized bottleneck. With regard to the allopolyploids, in the youngest D. purpurella both genome size and TE composition appear to be largely additive with respect to parents, whereas for polyploids of intermediate ages we uncover rampant genome expansion on a magnitude of multiple entire genomes of some plants such as Arabidopsis. The oldest allopolyploids in the series are not larger than the intermediate ones. A putative tandem repeat, potentially derived from a non-autonomous miniature inverted-repeat TE (MITE) drives much of the genome dynamics in the allopolyploids. The highly dynamic MITE-like element is found in higher proportions in the maternal diploid, D. fuchsii, but is observed to increase in copy number in both subgenomes of the allopolyploids. Altogether, the fate of repeats appears strongly regulated and therefore predictable across multiple independent allopolyploidization events in this system. Apart from the MITE-like element, we consistently document a mild genomic shock following the allopolyploidizations investigated here, which may be linked to their relatively large genome sizes, possibly associated with strong selection against further genome expansions.
DNA circuits compatible encoder and demultiplexer based on a single biomolecular platform with DNA strands as outputs
Authors: Xie Tianci , Deng Yuhan , Zhang Jiarui , Zhang Zhen , Hu Zhe , Wu Tongbo 
Published: July 2022

Abstract
A series of multiple logic circuits based on a single biomolecular platform is constructed to perform nonarithmetic and arithmetic functions, including 4-to-2 encoder, 1-to-2 demultiplexer, 1-to-4 demultiplexer, and multi-input OR gate. The encoder to a DNA circuit is the equivalent of a sensory receptor to a reflex arc. They all function to encode information from outside the pathway (DNA circuit or reflex arc) into a form that subsequent pathways can recognize and utilize. Current molecular encoders are based on optical or electrical signals as outputs, while DNA circuits are based on DNA strands as transmission signals. The output of existing encoders cannot be recognized by subsequent DNA circuits. It is the first time the DNA-based encoder with DNA strands as outputs can be truly applied to the DNA circuit, enabling the application of DNA circuits in non-binary biological environments. Another novel feature of the designed system is that the developed nanodevices all have a simple structure, low leakage and low crosstalk, which allows them to implement higher-level encoders and demultiplexers easily. Our work is based on the idea of complex functionality in a simple form, which will also provide a new route for developing advanced molecular logic circuits.