bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of intrinsic alignments on clustering constraints of the growth rate
Authors: Zwetsloot Karel , Chisari Nora Elisa 
Published: August 2022

ABSTRACT
Intrinsic alignments between galaxies and the large-scale structure contaminate galaxy clustering analyses and impact constraints on galaxy bias and the growth rate of structure in the Universe. This is the result of alignments inducing a selection effect on spectroscopic samples which is correlated with the large-scale structure. In this work, we quantify the biases on galaxy bias and the growth rate when alignments are neglected. We also examine different options for the mitigation of alignments by considering external priors on the effect and different probe combinations. We find that conservative analyses that restrict to kmax = 0.1 Mpc−1 are not significantly affected. However, analyses that aim to go to higher wave numbers could evidence a significant contamination from alignments. In those cases, including a prior on alignment amplitude, or combining clustering with the position-intrinsic shape correlation of galaxies, can recover the same expected constraining power, or even inform bias and growth rate measurements.
The sensitivity of the redshift distribution to galaxy demographics
Authors: Sudek Philipp , de la Bella Lucia F , Amara Adam , Hartley William G 
Published: August 2022

ABSTRACT
Photometric redshifts are commonly used to measure the distribution of galaxies in large surveys. However, the demands of ongoing and future large-scale cosmology surveys place very stringent limits on the redshift performance that are difficult to meet. A new approach to meet this precision need is forward modelling, which is underpinned by realistic simulations. In the work presented here, we use simulations to study the sensitivity of redshift distributions to the underlying galaxy population demographics. We do this by varying the redshift evolving parameters of the Schechter function for two galaxy populations: star-forming and quenched galaxies. Each population is characterized by eight parameters. We find that the redshift distribution of shallow surveys, such as the Sloan Digital Sky Survey (SDSS), is mainly sensitive to the parameters for quenched galaxies. However, for deeper surveys such as the Dark Energy Survey (DES) and the Hyper Suprime-Cam (HSC), the star-forming parameters have a stronger impact on the redshift distribution. Specifically, the slope of the characteristic magnitude, aM, for star-forming galaxies has overall the strongest impact on the redshift distribution. Decreasing aM by 148 per cent (its given uncertainty) shifts the mean redshift by ∼45 per cent. We explore which combination of colour and magnitude measurements is most sensitive to aM and we find that each colour–magnitude pair studied is similarly affected by a modification of aM.
Optical spectroscopy of the extremely metal-deficient star-forming galaxy HSC J1631+4426: a test of the strong-line method
Authors: Thuan T X , Guseva N G , Izotov Y I 
Published: August 2022

ABSTRACT
Recently, Kojima and co-authors have reported a record low oxygen abundance, 12 + logO/H = 6.90 ± 0.03, or 1.6 per cent of solar metallicity, in the low-mass star-forming galaxy HSC J1631 + 4426. This exceptionally low oxygen abundance was obtained by the direct method, using the [O iii]λ4363Å emission line. However, using the strong-line method by Izotov et al. (2019b), these authors have derived a significantly higher metallicity 12 + logO/H = 7.175 ± 0.005. To clarify the situation, we have obtained new observations of HSC J1631 + 4426 with the Large Binocular Telescope (LBT)/Multi-Object Dual Spectrograph (MODS). We have derived a higher oxygen abundance, 12 + logO/H = 7.14 ± 0.03, using the direct method, a value similar to the oxygen abundance obtained by the strong-line method. Thus, HSC J1631 + 4426 has a metallicity close to that of the well known blue compact dwarf galaxy I Zw 18.
Origin and Evolution of Nitrogen Fixation in Prokaryotes
Authors: Pi Hong-Wei , Lin Jinn-Jy , Chen Chi-An , Wang Po-Hsiang , Chiang Yin-Ru , Huang Chieh-Chen , Young Chiu-Chung , Li Wen-Hsiung 
Published: August 2022

AbstractThe origin of nitrogen fixation is an important issue in evolutionary biology. While nitrogen is required by all living organisms, only a small fraction of bacteria and archaea can fix nitrogen. The prevailing view is that nitrogen fixation first evolved in archaea and was later transferred to bacteria. However, nitrogen-fixing (Nif) bacteria are far larger in number and far more diverse in ecological niches than Nif archaea. We, therefore, propose the bacteria-first hypothesis, which postulates that nitrogen fixation first evolved in bacteria and was later transferred to archaea. As &gt;30,000 prokaryotic genomes have been sequenced, we conduct an in-depth comparison of the two hypotheses. We first identify the six genes involved in nitrogen fixation in all sequenced prokaryotic genomes and then reconstruct phylogenetic trees using the six Nif proteins individually or in combination. In each of these trees, the earliest lineages are bacterial Nif protein sequences and in the oldest clade (group) the archaeal sequences are all nested inside bacterial sequences, suggesting that the Nif proteins first evolved in bacteria. The bacteria-first hypothesis is further supported by the observation that the majority of Nif archaea carry the major bacterial Mo (molybdenum) transporter (ModABC) rather than the archaeal Mo transporter (WtpABC). Moreover, in our phylogeny of all available ModA and WtpA protein sequences, the earliest lineages are bacterial sequences while archaeal sequences are nested inside bacterial sequences. Furthermore, the bacteria-first hypothesis is supported by available isotopic data. In conclusion, our study strongly supports the bacteria-first hypothesis.
Distinct, opposing functions for CFIm59 and CFIm68 in mRNA alternative polyadenylation of Pten and in the PI3K/Akt signalling cascade
Authors: Tseng Hsin-Wei , Mota-Sydor Anthony , Leventis Rania , Jovanovic Predrag , Topisirovic Ivan , Duchaine Thomas F 
Published: August 2022

Abstract
Precise maintenance of PTEN dosage is crucial for tumor suppression across a wide variety of cancers. Post-transcriptional regulation of Pten heavily relies on regulatory elements encoded by its 3′UTR. We previously reported the important diversity of 3′UTR isoforms of Pten mRNAs produced through alternative polyadenylation (APA). Here, we reveal the direct regulation of Pten APA by the mammalian cleavage factor I (CFIm) complex, which in turn contributes to PTEN protein dosage. CFIm consists of the UGUA-binding CFIm25 and APA regulatory subunits CFIm59 or CFIm68. Deep sequencing analyses of perturbed (KO and KD) cell lines uncovered the differential regulation of Pten APA by CFIm59 and CFIm68 and further revealed that their divergent functions have widespread impact for APA in transcriptomes. Differentially regulated genes include numerous factors within the phosphoinositide 3-kinase (PI3K)/protein kinase B (Akt) signalling pathway that PTEN counter-regulates. We further reveal a stratification of APA dysregulation among a subset of PTEN-driven cancers, with recurrent alterations among PI3K/Akt pathway genes regulated by CFIm. Our results refine the transcriptome selectivity of the CFIm complex in APA regulation, and the breadth of its impact in PTEN-driven cancers.
Armed conflicts and kidney patients: a consensus statement from the Renal Disaster Relief Task Force of the ERA
Authors: Sever Mehmet S , Vanholder Raymond , Luyckx Valerie , Eckardt Kai-Uwe , Kolesnyk Mykola , Wiecek Andrzej , Pawlowicz-Szlarska Ewa , Gallego Daniel , Shroff Rukshana , Škoberne Andrej , Nistor Ionut , Sekkarie Mohamed , Ivanov Dmytro , Noruišiene Edita , Tuglular Serhan 
Published: August 2022

ABSTRACT
During conflicts, people with kidney disease, either those remaining in the affected zones or those who are displaced, may be exposed to additional threats because of medical and logistical challenges. Acute kidney injury developing on the battlefield, in field hospitals or in higher-level hospital settings is characterized by poor outcomes. People with chronic kidney disease may experience treatment interruptions, contributing to worsening kidney function. Patients living on dialysis or with a functioning graft may experience limitations of dialysis possibilities or availability of immunosuppressive medications, increasing the risk of severe complications including death. When patients must flee, these threats are compounded by unhealthy and insecure conditions both during displacement and/or at their destination. Measures to attenuate these risks may only be partially effective. Local preparedness for overall and medical/kidney-related disaster response is essential. Due to limitations in supply, adjustments in dialysis frequency or dose, switching between hemodialysis and peritoneal dialysis and changes in immunosuppressive regimens may be required. Telemedicine (if possible) may be useful to support inexperienced local physicians in managing medical and logistical challenges. Limited treatment possibilities during warfare may necessitate referral of patients to distant higher-level hospitals, once urgent care has been initiated. Preparation for disasters should occur ahead of time. Inclusion of disaster nephrology in medical and nursing curricula and training of patients, families and others on self-care and medical practice in austere settings may enhance awareness and preparedness, support best practices adapted to the demanding circumstances and prepare non-professionals to lend support.
National-level overall survival patterns for molecularly-defined diffuse glioma types in the United States
Authors: Ostrom Quinn T , Shoaf Madison L , Cioffi Gino , Waite Kristin , Kruchko Carol , Wen Patrick Y , Brat Daniel J , Barnholtz-Sloan Jill S , Iorgulescu J Bryan 
Published: August 2022

AbstractBackgroundMolecularly-defined diffuse glioma types—including IDH-wildtype glioblastoma, IDH-mutant astrocytoma, IDH-mutant 1p/19q-codeleted oligodendroglioma, and H3 K27M-mutant diffuse midline glioma—were incorporated into U.S. cancer registry reporting for individuals with brain tumors beginning in 2018. We leveraged these new data to estimate the national-level overall survival (OS) patterns associated with glioma integrated diagnoses.MethodsIndividuals diagnosed with diffuse gliomas in 2018 and had brain molecular marker data were identified within the U.S. National Cancer Database. OS was estimated using Kaplan–Meier methods and stratified by WHO CNS grade, age, sex, tumor size, treatment, extent of resection, and MGMT promoter methylation. Additionally, the effects of WHO CNS grade were examined among individuals with IDH-wildtype astrocytic gliomas.Results8651 individuals were identified. One-year OS was 53.7% for WHO grade 4 IDH-wildtype glioblastomas; 98.0%, 92.4%, and 76.3% for WHO grade 2, 3, and 4 IDH-mutant astrocytomas, respectively; 97.9% and 94.4% for WHO grade 2 and 3 IDH-mutant 1p/19q-codeleted oligodendrogliomas, respectively; and 55.9% for H3 K27M-mutant diffuse midline gliomas. Among IDH-wildtype glioblastomas, median OS was 17.1 months and 12.4 months for methylated and unmethylated MGMT promoters. Additionally, IDH-wildtype diffuse astrocytic gliomas reported as WHO grade 2 or 3 demonstrated longer OS compared to grade 4 tumors (both P &lt; .001).ConclusionsOur findings provide the initial national OS estimates for molecularly-defined diffuse gliomas in the United States and illustrate the importance of incorporating such data into cancer registry reporting.
Sexually Transmitted Infection Testing in the National Veterans Health Administration Patient Cohort During the Coronavirus Disease 2019 Pandemic
Authors: Beste Lauren A , Keddem Shimrit , Borgerding Joleen , Lowy Elliott , Gardella Carolyn , McFarland Lorenzo , Comstock Emily , Fonseca Giuseppe Allan , Van Epps Puja , Ohl Michael , Hauser Ronald G , Ross David , Maier Marissa M 
Published: August 2022

AbstractBackgroundWe performed a retrospective study of chlamydia, gonorrhea, syphilis, and human immunodeficiency virus (HIV) testing in the Veterans Health Administration (VHA) during 2019–2021.MethodsWe determined the annual number of chlamydia, gonorrhea, syphilis, and HIV tests from 2019 through 2021 using electronic health record data. We calculated rates by age, birth sex, race, census region, rurality, HIV status, and use of preexposure prophylaxis.ResultsThe VHA system experienced a 24% drop in chlamydia/gonorrhea testing, a 25% drop in syphilis testing, and a 29% drop in HIV testing in 2020 versus 2019. By the conclusion of 2021, testing rates had recovered to 90% of baseline for chlamydia/gonorrhea, 91% for syphilis, and 88% for HIV. Declines and subsequent improvements in sexually transmitted infection (STI) testing occurred unequally across age, sex, race, and geographic groups. Testing for all 4 STIs in 2021 remained below baseline in rural Veterans. Excluding those aged &lt;25 years, women experienced a steeper decline and slower recovery in chlamydia/gonorrhea testing relative to men, but quicker recovery in HIV testing. Asian Americans and Hawaiian/Pacific Islanders had a steeper decline and a slower recovery in testing for chlamydia/gonorrhea. Black and White Veterans had slower recovery in HIV testing compared with other race groups. People living with HIV experienced a smaller drop in testing for syphilis compared with people without HIV, followed by a near-total recovery of testing by 2021.ConclusionsAfter dramatic reductions from 2019 to 2020, STI testing rates returned to near-baseline in 2021. Testing recovery lagged in rural, female, Asian American, Hawaiian/Pacific Islander, and Black Veterans.
Stomatal Development and Gene Expression in Rice Florets
Authors: Bertolino Lígia T , Caine Robert S , Zoulias Nicholas , Yin Xiaojia , Chater Caspar C C , Biswal Akshaya , Quick William P , Gray Julie E 
Published: August 2022

Abstract
Stomata play a fundamental role in modulating the exchange of gases between plants and the atmosphere. These microscopic structures form in high numbers on the leaf epidermis and are also present on flowers. Although leaf stomata are well studied, little attention has been paid to the development or function of floral stomata. Here, we characterize in detail the spatial distribution and development of the floral stomata of the indica rice variety IR64. We show that stomatal complexes are present at low density on specific areas of the lemma, palea and anthers and are morphologically different compared to stomata found on leaves. We reveal that in the bract-like organs, stomatal development follows the same cell lineage transitions as in rice leaves and demonstrate that the overexpression of the stomatal development regulators OsEPFL9-1 and OsEPF1 leads to dramatic changes in stomatal density in rice floral organs, producing lemma with approximately twice as many stomata (OsEPFL9-1_oe) or lemma where stomata are practically absent (OsEPF1_oe). Transcriptomic analysis of developing florets also indicates that the cellular transitions during the development of floral stomata are regulated by the same genetic network used in rice leaves. Finally, although we were unable to detect an impact on plant reproduction linked to changes in the density of floral stomata, we report alterations in global gene expression in lines overexpressing OsEPF1 and discuss how our results reflect on the possible role(s) of floral stomata.
BORON-ENHANCED BIOLOGICAL EFFECTIVENESS OF PROTON IRRADIATION: STRATEGY TO ASSESS THE UNDERPINNING MECHANISM
Authors: Kundrát Pavel , Pachnerová Brabcová Kateřina , Jelínek Michaelidesová Anna , Zahradníček Oldřich , Danilová Irina , Štěpán Václav , Jamborová Zuzana , Davídková Marie 
Published: August 2022

Abstract
Proton radiotherapy for the treatment of cancer offers an excellent dose distribution. Cellular experiments have shown that in terms of biological effects, the sharp dose distribution is further amplified, by as much as 75%, in the presence of boron. It is a matter of debate whether the underlying physical processes involve the nuclear reaction of 11B with protons or 10B with secondary neutrons, both producing densely ionizing short-ranged particles. Likewise, potential roles of intercellular communication or boron acting as a radiosensitizer are not clear. We present an ongoing research project based on a multiscale approach to elucidate the mechanism by which boron enhances the effectiveness of proton irradiation in the Bragg peak. It combines experimental with simulation tools to study the physics of proton–boron interactions, and to analyze intra- and inter-cellular boron biology upon proton irradiation.
THE IMPORTANCE OF FEEDBACK IN MONITORING PATIENTS’ RADIATION DOSES IN MAMMOGRAPHY
Authors: Horváthová Martina , Bárdyová Zuzana , Gomola Igor 
Published: August 2022

Abstract
The majority of medical facilities in the Slovak Republic archive diagnostic images of their patients in a picture archiving and communicating system (PACS). Data from the PACS system can be used to analyse patient radiation dose and perform internal and external quality control through dose monitoring software systems. However, appropriate use of such systems requires the provision of feedback and the ability of staff to identify causes of diagnostic reference level exceedances. The present pilot study evaluated the use of a Dose quality control system (DQC) for monitoring the radiation dose of the patients in the ongoing mammography screening, with subsequent identification of alerts triggered by the system.
OPTIMISATION OF ABDOMINAL CT EXAM PROTOCOLS IN OBESE PATIENTS
Authors: Balogová Zdenka , Súkupová Lucie 
Published: August 2022

Abstract
Obesity is marked as a global epidemic, and the number of obese people is steadily increasing. This disease affects various aspects of health care, which also includes radiodiagnostic imaging modalities. CT exams of bariatric patients are becoming common in radiological practice and bring problems of both technical and physical nature. Obesity affects the quality of CT images, therefore, optimisation of the used CT protocols is important, which is difficult to be carried out on patients, because of the principles of radiation protection and ethical point of view. This study evaluates and compares three available CT protocols for examination of the abdomen in terms of image quality, radiation dose and scan time on two CT scanners of the manufacturer Siemens. For optimisation, an anthropomorphic phantom of the abdomen was used, which, by its size and attenuation of the used materials, suitably simulated an obese patient.
SPACEDOS: AN OPEN-SOURCE PIN DIODE DOSEMETER FOR APPLICATIONS IN SPACE
Authors: Kákona Martin , Ambrožová Iva , Inozemtsev Konstantin O , Ploc Ondřej , Tolochek Raisa V , Sihver Lembit , Velychko Olena , Chroust Jan , Kitamura Hisashi , Kodaira Satoshi , Shurshakov Vyacheslav A 
Published: August 2022

Abstract
A new Open-Source dosemeter, SPACEDOS, has been developed for measurements of cosmic radiation on board spacecraft and small satellites. Its main advantages are that it is small and lightweight with low power consumption. It can be adjusted for specific applications, e.g. used in pressurized cabins of spacecraft or in vacuum environments in CubeSats or larger satellites. The open-source design enables better portability and reproduction of the results than other similar detectors. The detector has already successfully performed measurements on board the International Space Station. The obtained results are discussed and compared with those measured with thermoluminescent detectors located in the same position as SPACEDOS.
RADIOCARBON DATING OF CHARCOALS FROM HISTORICAL MORTARS FROM TÝŘOV AND PYŠOLEC CASTLES
Authors: Pachnerová Brabcová Kateřina , Krofta Tomáš , Valášek Vojtěch , Suchý Václav , Kundrát Pavel , Šimek Pavel , Kozlovcev Petr , Kotková Kristýna , Fialová Anna , Povinec Pavel P , Válek Jan , Světlík Ivo 
Published: August 2022

Abstract
Organic inclusions in lime binders provide useful samples for radiocarbon dating of historical objects. Two Czech castles Týřov and Pyšolec from Late Middle Ages were explored, and tens of charcoals were found in their walls. The radiocarbon content of the charcoals was measured with accelerator mass spectrometry. The dating results showed that none of the charcoals were younger than the known historical ages (Týřov: 1260 - 1270, Pyšolec: 1300 - 1340), but some were considerably older. Two charcoals from Pyšolec castle dated to Palaeolithic, likely originating from fluvial sediments added as an aggregate to the mortar. When excluding these two charcoals, the others indicated most likely dates being 50–100 y older than the building dates of the castles. This systemic effect corresponds to the age of wood used for lime burning and shall be accounted for when dating mortars using charcoals.
MODELING AND OPTIMIZATION OF HPGE DETECTOR GC0518 USING MCNP5 CODE
Authors: Stríbrnský Branislav , Hinca Róbert , Farkas Gabriel , Petriska Martin , Slugeň Vladimír 
Published: August 2022

Abstract
For precise modeling of a high purity germanium (HPGe) detector, detailed knowledge of its geometry is necessary. Unfortunately, some of the detector geometric parameters are often not available. This study suggests simple procedures for determining geometry without the need for radiography. The study considers the HPGe detector GC0518 manufactured by Mirion. The detector datasheet is available, but the uncertainties do not allow the detector to be modeled without additional corrections. The detector was modeled using MCNP5 code and the results were compared with calibration point sources and Marinelli beakers measurements. We also performed measurements to obtain information on the germanium dead layer, crystal holder shape, inner hole shape and radii of the crystal edges. Then the model was optimized according to the measurements. Finally, the full energy peak efficiencies were evaluated. The relative differences between the measured and calculated efficiencies are less than 4.5% for point sources and 5.4% for Marinelli beakers.
MONTE CARLO SIMULATION OF POLONIUM ION COLLECTION IN ELECTROSTATIC FIELD FOR THE PURPOSE OF RADON DETECTOR DEVELOPMENT
Authors: Kaschner Martin , Kafka Vladimír , Marčišovský Michal , Staněk Pavel , Švihra Peter 
Published: August 2022

Abstract
Radon detectors based on an electrostatic collection of polonium and detection of its alpha decay are a popular choice for the measurement of radon activity. Due to the nature of $^{222}$Rn decays, 88% of radon progeny have a positive charge, thus enabling their collection on an electrode. A simulation software focused on the drift and diffusion of ions in an electric field has been developed, providing a tool to study and characterise such detectors. It has been found that one such device achieves only 44% collection efficiency, caused by the loss of a large fraction of the ions before reaching the collection diode. An improvement of the design is therefore proposed, changing the placement of the sensor resulted in an simulated increase of the collection efficiency up to 93%. Preliminary measurements performed using prototypes of these detectors confirm the results of the simulations.