bluuebunny/crossref_metadata_2025_split huggingface dataset:
Imaging indigenous sacred sites: A tale of clay, silt, and sand
Authors: Nobes David C. 
Published: September 2021

When studying indigenous sites, especially sacred sites such as burials, the needs and wishes of the indigenous people are paramount; the site integrity must be respected, and the site must be left intact and undisturbed. Noninvasive, nondestructive geophysical imaging is well suited to such investigations, but suspicion within indigenous communities because of past transgressions is a barrier to widespread use; skepticism is not uncommon, but we have always managed to convince skeptics. We have developed an overview of results from 10 Māori (the indigenous peoples of New Zealand) sites in the South Island of New Zealand: one historic burial site, six modern burial sites that also had historical use, one historic battle site, one prehistoric site that may have been a burial site, and one prehistoric site used for food storage that was tapu (sacred). Our approach was to let them ask us to delineate areas of importance, for example, old burial sites. There are, naturally, processes and protocols, cultural and technical, that we followed. The sites comprised a range of lithologies and soil types: one site where clay soil overlays limestone, five sites where loess (airborne silt) overlays basalt, one set of inland silty soil sites, one site on peat soils overlying sandy gravels, and two sites in coastal sands. The geophysical responses of the sites cluster into three groups: Horizontal loop electromagnetic (HLEM) and magnetic field methods worked well for the clay soil site, and once the effects of the conductive clay response were removed by filtering, ground-penetrating radar (GPR) worked well. HLEM and magnetic results were good to equivocal on the silty and peaty sites, whereas GPR excelled at delineating anomalous features, particularly burials, which yielded clear characteristic diffraction responses. Finally, results for coastal sand sites were disappointing. Such sites appear to be too dynamic to yield useful results.
Dynamic Changes of Circulating Tumor DNA Predict Clinical Outcome in Patients With Advanced Non–Small-Cell Lung Cancer Treated With Immune Checkpoint Inhibitors
Authors: Weber Sabrina , van der Leest Paul , Donker Hylke C. , Schlange Thomas , Timens Wim , Tamminga Menno , Hasenleithner Samantha O. , Graf Ricarda , Moser Tina , Spiegl Benjamin , Yaspo Marie-Laure , Terstappen Leon W. M. M. , Sidorenkov Grigory , Hiltermann T. Jeroen. N. , Speicher Michael R. , Schuuring Ed , Heitzer Ellen , Groen Harry J. M. 
Published: September 2021

PURPOSE Immune checkpoint inhibitors (ICIs) are increasingly being used in non–small-cell lung cancer (NSCLC), yet biomarkers predicting their benefit are lacking. We evaluated if on-treatment changes of circulating tumor DNA (ctDNA) from ICI start (t0) to after two cycles (t1) assessed with a commercial panel could identify patients with NSCLC who would benefit from ICI. PATIENTS AND METHODS The molecular ctDNA response was evaluated as a predictor of radiographic tumor response and long-term survival benefit of ICI. To maximize the yield of ctDNA detection, de novo mutation calling was performed. Furthermore, the impact of clonal hematopoiesis (CH)–related variants as a source of biologic noise was investigated. RESULTS After correction for CH-related variants, which were detected in 75 patients (44.9%), ctDNA was detected in 152 of 167 (91.0%) patients. We observed only a fair agreement of the molecular and radiographic response, which was even more impaired by the inclusion of CH-related variants. After exclusion of those, a ≥ 50% molecular response improved progression-free survival (10 v 2 months; hazard ratio [HR], 0.55; 95% CI, 0.39 to 0.77; P = .0011) and overall survival (18.4 v 5.9 months; HR, 0.44; 95% CI, 0.31 to 0.62; P < .0001) compared with patients not achieving this end point. After adjusting for clinical variables, ctDNA response and STK11/ KEAP1 mutations (HR, 2.08; 95% CI, 1.4 to 3.0; P < .001) remained independent predictors for overall survival, irrespective of programmed death ligand-1 expression. A landmark survival analysis at 2 months (n = 129) provided similar results. CONCLUSION On-treatment changes of ctDNA in plasma reveal predictive information for long-term clinical benefit in ICI-treated patients with NSCLC. A broader NSCLC patient coverage through de novo mutation calling and the use of a variant call set excluding CH-related variants improved the classification of molecular responders, but had no significant impact on survival.
Molecular Tumor Board Review and Improved Overall Survival in Non–Small-Cell Lung Cancer
Authors: Huang Bin , Chen Quan , Allison Derek , El Khouli Riham , Peh Keng Hee , Mobley James , Anderson Abigail , Durbin Eric B. , Goodin Donald , Villano John L. , Miller Rachel W. , Arnold Susanne M. , Kolesar Jill M. 
Published: September 2021

PURPOSEWith the introduction of precision medicine, treatment options for non–small-cell lung cancer have improved dramatically; however, underutilization, especially in disadvantaged patients, like those living in rural Appalachian regions, is associated with poorer survival. Molecular tumor boards (MTBs) represent a strategy to increase precision medicine use. UK HealthCare at the University of Kentucky (UK) implemented a statewide MTB in January 2017. We wanted to test the impact of UK MTB review on overall survival in Appalachian and other regions in Kentucky.METHODSWe performed a case-control study of Kentucky patients newly diagnosed with non–small-cell lung cancer between 2017 and 2019. Cases were reviewed by the UK MTB and were compared with controls without UK MTB review. Controls were identified from the Kentucky Cancer Registry and propensity-matched to cases. The primary end point was the association between MTB review and overall patient survival.RESULTSOverall, 956 patients were included, with 343 (39%) residing in an Appalachian region. Seventy-seven (8.1%) were reviewed by the MTB and classified as cases. Cox regression analysis showed that poorer survival outcome was associated with lack of MTB review (hazard ratio [HR] = 8.61; 95% CI, 3.83 to 19.31; P < .0001) and living in an Appalachian region (hazard ratio = 1.43; 95% CI, 1.17 to 1.75; P = .004). Among individuals with MTB review, survival outcomes were similar regardless of whether they lived in Appalachia or other parts of Kentucky.CONCLUSIONMTB review is an independent positive predictor of overall survival regardless of residence location. MTBs may help overcome some health disparities for disadvantaged populations.
A novel kind of equations linking the quantum dynamics and the classical wave motions based on the catastrophe theory
Authors: Wu Jiu Hui , Zhang Lin , Zhou Ke jiang 
Published: September 2021

Abstract
Considering that the catastrophe theory could describe quantitatively any phase transition process, we adopt the folding and cusp catastrophe types as the potential functions in the Schrödinger equation to attempt to link the quantum dynamics and the classical wave motions. Thus, through the dimensionless analysis a novel kind of partial differential equations is derived out. When the scaling parameter of the novel equation is equal to the Planck's constant, this equation becomes a detailed time-independent Schrödinger equation, from which Bohr correspondence principle can be found. On the other hand, when the scaling parameter tends to zero, this equation could degenerate to the classical Helmholtz equation. Therefore, this novel kind of equations could describe quantitatively the variation process of the wave functions from the macroscopic level to the quantum size.
Coupling-modulation–mediated generation of stable entanglement of superconducting qubits via dissipation
Authors: Ma Sheng-li , Zhang Jing , Li Xin-ke , Ren Ya-long , Xie Ji-kun , Cao Ming-tao , Li Fu-li 
Published: September 2021

Abstract
We propose an experimentally feasible scheme for the dissipative generation of stable entanglement of superconducting qubits via coupling modulation without applying any drives on qubits and resonator. Firstly, we study the circuit of one superconducting transmission line resonator coupled to two separated qubits via two superconducting quantum interference devices (SUQIDs). By modulating the inductance of the SQUIDs via external fluxes, we can tailor an appropriate qubit-resonator coupling with both red- and blue-sideband interactions. Combined with the photon loss of the resonator, the two qubits can be autonomously steered into a long-lived entangled state with high fidelity. Moreover, we extend the model to one resonator coupled to two separated qubit chains, each of which contains N linearly coupled superconducting qubits. We show that the lossy resonator can drive the whole system into a unique dark state, i.e., a series of N entangled pairs of qubits across the chains can be stabilized at the stationary state. So, the present work enables the preparation of a stable long-range entangled state between the two qubits in the end sites of the chains, which plays an important role for implementing scalable quantum computation and quantum communication.
Engineering chromosome rearrangements in cancer
Authors: Alonso Salvador , Dow Lukas E. 
Published: September 2021

ABSTRACT
The identification of large chromosomal rearrangements in cancers has multiplied exponentially over the last decade. These complex and often rare genomic events have traditionally been challenging to study, in part owing to lack of tools that efficiently engineer disease-associated inversions, deletions and translocations in model systems. The emergence and refinement of genome editing technologies, such as CRISPR, have significantly expanded our ability to generate and interrogate chromosomal aberrations to better understand the networks that govern cancer growth. Here we review how existing technologies are employed to faithfully model cancer-associated chromosome rearrangements in the laboratory, with the ultimate goal of developing more accurate pre-clinical models of and therapeutic strategies for cancers driven by these genomic events.
LRRC23 is a conserved component of the radial spoke that is necessary for sperm motility and male fertility in mice
Authors: Zhang Xin , Sun Jiang , Lu Yonggang , Zhang Jintao , Shimada Keisuke , Noda Taichi , Zhao Shuqin , Koyano Takayuki , Matsuyama Makoto , Zhou Shushu , Wu Jiayan , Ikawa Masahito , Liu Mingxi 
Published: September 2021

ABSTRACT
Cilia and flagella are ancient structures that achieve controlled motor functions through the coordinated interaction based on microtubules and some attached projections. Radial spokes (RSs) facilitate the beating motion of these organelles by mediating signal transduction between dyneins and a central pair (CP) of singlet microtubules. RS complex isolation from Chlamydomonas axonemes enabled the detection of 23 radial spoke proteins (RSP1–RSP23), although the roles of some radial spoke proteins remain unknown. Recently, RSP15 has been reported to be bound to the stalk of RS2, but its homolog in mammals has not been identified. Herein, we show that Lrrc23 is an evolutionarily conserved testis-enriched gene encoding an RSP15 homolog in mice. We found that LRRC23 localizes to the RS complex within murine sperm flagella and interacts with RSPH3A and RSPH3B. The knockout of Lrrc23 resulted in male infertility due to RS disorganization and impaired motility in murine spermatozoa, whereas the ciliary beating was not significantly affected. These data indicate that LRRC23 is a key regulator that underpins the integrity of the RS complex within the flagella of mammalian spermatozoa, whereas it is dispensable in cilia.
This article has an associated First Person interview with the first author of the paper.
Coronary flow quantification estimated by dynamic 320-detector CT angiography: validation by 13N ammonia PET myocardial flow reserve
Authors: Matsuo Yuka , Nagao Michinobu , Yamamoto Atsushi , Ando Kiyoe , Nakao Risako , Fukushima Kenji , Momose Mitsuru , Sakai Akiko , Sato Kayoko , Sakai Shuji 
Published: September 2021

Objectives: Resting coronary flow index (rCFI) estimated by 320-detector low-dose dynamic coronary CT angiography (CCTA) is a direct flow quantification using intracoronary attenuation. We propose modified-rCFI from new protocol combining dynamic scan and standard CCTA using dose-modulation, and validate its consistency with quantitative values and ischemia depicted by 13N-ammonia PET (NH3-PET). Methods: 46 patients who underwent dynamic CCTA and NH3-PET for coronary artery disease were evaluated using original rCFI in 21 patients and modified-rCFI in 25 patients. Two types of rCFI were calculated for three major coronary arteries. Myocardial blood flow (MBF) at rest and stress, myocardial flow reserve (MFR), and the presence or absence of ischemia for three major territories were depicted by NH3-PET. Coronary territories were categorized as territories with MFR <2.0, ≥2.0, or with and without ischemia. Receiver operating characteristic analysis was performed to determine the optimal cut-off of rCFI to distinguish territories with MFR <2.0 or the presence of ischemia. Results: rCFI and modified-rCFI had significant positive correlations with stress MBF and MFR. The optical cut-offs of rCFI and modified-rCFI of 0.39 and 0.61 could detect territories with MFR <2.0, with AUCs of 0.75 and 0.73, sensitivities of 48 and 34%, and specificities of 97 and 98%. Optimal cut-offs of rCFI and modified-rCFI distinguished ischemic segments from non-ischemic segments, with AUCs of 0.75 and 0.91, sensitivities of 53 and 50%, and specificities of 93 and 95%. Conclusion: Two types of rCFI correlated with quantitative values from NH3-PET, and were consistent with a high specificity in detecting functional ischemia. Advances in knowledge: rCFI can contribute as additional functional test over standard CCTA in clinical work-up.
Neogene-Quaternary tectonic regime and macroseismic observations in the Tyrnavos-Elassona broader epicentral area of the March 2021, intense earthquake sequence
Authors: Galanakis Dimitrios , Sboras Sotiris , Konstantopoulou Garyfalia , Xenakis Markos 
Published: September 2021

On March 3, 2021, a strong (Mw6.3) earthquake occurred near the towns of Tyrnavos and Elassona. One day later (March 4), a second strong (Mw6.0) earthquake occurred just a few kilometres toward the WNW. The aftershock spatial distribution and the focal mechanisms revealed NW-SE-striking normal faulting. The focal mechanisms also revealed a NE-SW oriented extensional stress field, different from the orientation we knew so far (ca. N-S). The magnitude and location of the two strongest shocks, and the spatiotemporal evolution of the sequence, strongly suggest that two adjacent fault segments were ruptured respectively. The sequence was followed by several coseismic ground deformational phenomena, such as landslides/rockfalls, liquefaction and ruptures. The landslides and rockfalls were mostly associated with the ground shaking. The ruptures were observed west of the Titarissios River, near to the Quaternary faults found by bore-hole lignite investigation. In the same direction, a fault scarp separating the alpidic basement from the alluvial deposits of the Titarissios valley implies the occurrence of a well-developed fault system. Some of the ground ruptures were accompanied by extensive liquefaction phenomena. Others cross-cut reinforced concrete irrigation channels without changing their direction. We suggest that this fault system was partially reactivated, as a secondary surface rupture, during the sequence as a steeper splay of a deeper low-to-moderate angle normal fault.
ВОЗРАСТНЫЕ ИЗМЕНЕНИЯ УРОВНЯ ЭКСПРЕССИИ МАРКЕРОВ ПЛОТНЫХ КОНТАКТОВ У ЖЕНЩИН ПОСЛЕ МИОМЭКТОМИИ
Authors: Shapovalova Alexandra I. , Polyakova Viktoria O. , Kleimenova Tatyana S. 
Published: September 2021

Обоснование. Миома матки представляет собой доброкачественные опухоли, образующиеся из гладкомышечных клеток. Клаудины (CLDN) являются основными белками плотных контактов, демонстрируя различную экспрессию в тканях, причем профиль экспрессии CLDN является репрезентативным. CLDN играют важнейшую роль в неопластических процессах, так как принимают участие в формировании единого сигнального пути между внеклеточным матриксом и внутриклеточным цитоскелетом.
Цель. Изучить уровень экспрессии маркеров, отвечающих за функциональную активность плотных контактов клеток CLDN1, CLDN7 и CLDN10 в биоптатах интактного миометрия у женщин разных возрастных групп.
Материалы и методы. Обследовано 90 пациенток в возрасте от 23 до 47 лет, которые были рандоминизированы на 6 групп. В первые три группы вошли 45 практически здоровых пациенток, в четвертую, пятую и шестую группы – женщины с миомой матки. И контрольные группы и пациентки с миомой матки были разделены на ранний, средний и поздний репродуктивный возраст.
Исследование проводилось с разрешения этического комитета в отделении оперативной гинекологии с операционным блоком ФГБНУ «НИИ АГиР им. Д.О. Отта». (Директор – д.м.н., профессор Коган И.Ю.). Каждый участник подписывал форму информированного согласия на обследование.
Проведён комплекс диагностических методик: анамнестические данные, клинико-гинекологическое обследование, эхография, эндоскопия, гистологическое исследование соскобов и макропрепаратов, удаленных во время операций. Далее материал исследовался при помощи иммунофлуоресцентного анализа.
Статистическая обработка проводилась в программе «Excel 2010. Microsoft Office» и в аналитической программе «Statistica 10.0».
Результаты. В результате иммунофлуоренсцентного анализа было выявлено, что уровень экспрессии маркеров плотных межклеточных контактов Claudin 1, Claudin 7 и Claudin 10 снижается в эпителии мембран клеток у женщин, страдающих миомой матки.
Заключение. Таким образом, изменение функциональной активности плотных контактов приводит к нарушению связей между соседними клетками. Уровень экспрессии клаудинов может быть использован в качестве маркера и мишени для таргетной терапии.
Endodontic treatment regimens and their application in practice - survey and comparative study
Authors: Kula Łucja , Kalinowska Julita , Koczor-Rozmus Aleksandra 
Published: September 2021

Introduction: Endodontics is a rapidly developing field of dentistry. Dentists have an increasing selection of techniques, tools, and materials to ensure therapeutic success.Aim: The aim of the study was to analyze the endodontic treatment regimens and their application in the daily practice of dentists. Material and Methods: A dentist survey was conducted through a Google Doc. The link to the form was placed on online dental groups, sent by e-mail to the offices and the questionnaire was also delivered to the dental offices in a printed form.Results: The majority of respondents always perform endodontic treatment procedures on pregnant women, take three X-rays and use a rubber dam during the treatment. Almost all respondents have the opportunity to take an X-ray in the workplace, and the working length is usually measured by the electronic method. The most commonly used methods of root canal preparation are the traditional and crown-down methods, and the most commonly used root canal filling method - the thermal method. Most of the respondents declared the following rinsing protocol: NaOCl and CA or EDTA. Apex locator, ultrasounds, and microscopes are used in most dental offices, and more than half of the dentists responded that they perform procedures like broken tools removal or obliterated canals enlargement.Conclusions: Polish endodontics has developed over the years. Modern solutions are used more and more often. The canals are filled with the thermal method, and the popularity of performing complex endodontic procedures has increased. However, it is necessary to conduct further studies comparing the effectiveness of the canal preparation methods and the standardization of the root canal irrigation protocol.
Subjctive assessment of the quality of life of patients with rheumatological diseases
Authors: Tomaszewska Katarzyna , Majchrowicz Bożena , Szewczyk Magdalena 
Published: September 2021

Background: Nowadays, rheumatic diseases are increasingly recognized as chronic diseases that lead to disability, reduced quality of life and dependence on others. They are caused by pain, stiffness and reduced mobility in the joints. Early treatment and rehabilitation can improve quality of life, prolong functional abilities and independence.Objectives: Assessment of functioning and quality of life in patients with rheumatologic diseases.Material and methods: The study group consisted of 200 patients diagnosed with rheumatological disease. The research method was the diagnostic survey method. As a technique, the survey technique was used, and the tool for collecting data from patients was a questionnaire, consisting of two parts: a questionnaire and a standardized quality of life questionnaire SF-36.Results: By far the greatest in the study group of patients were limitations in the performance of roles due to physical health (score at the average level of 96.8%) and also limitations due to emotional problems (score at the average level of 72.0%) classified as high. The severity of the study patients' limitations in physical functioning (50.6%), severity of pain (56.0%), assessment of general health (53.0%) and vitality (53.5%) were rated at medium level. The study patients' limitations in social functioning (34.8%) and mental health (46.2%) were relatively low.Conclusions: The quality of life of patients with rheumatologic diseases is rated at an average level, the physical dimension was rated worse by older people and better by people with higher education.
Association Between Male fertility and Vitamin D
Authors: Piekarska Ewa , Pawlicki Mateusz , Łopuszyńska Anna , Kozioł Magdalena , Krasa Aleksandra , Piecewicz-Szczęsna Halina 
Published: September 2021

Introduction: Infertility affects millions of people of reproductive age worldwide. Male infertility may be caused by a number of different factors including problems in the ejection of semen, absence or low levels of sperm, or abnormal morphology and movement of the sperm. Environmental and lifestyle factors also have a meaningful impact on male reproductive system. Fertility care should include the prevention, diagnosis and treatment of the disorder. That is why numerous studies have explored the role of vitamin D in regulating the functioning of the reproductive system.Aim of study: Investigation of correlation between Vitamin D and male fertility.Results: Studies consistently show that Vitamin D deficiency has a negative influence on male fertility. Number of trials show that the mean value of Vitamin D serum levels tend to be significantly lower in infertile men compared to fertile men. Vitamin D insufficiency and deficiency has been noticed to be associated with poor semen quality (lower sperm concentrations, lower motility). It became evident that vitamin D exhibits positive correlation with the male fertility by maintaining the levels of sex hormones, down regulating oxidative stress and up regulating oxidative defence. Supplementation of Vitamin D may improve the quality and function of sperm by increasing its motility and concentration.Conclusions: Although Vitamin D supplementation cannot be considered for treatment of male infertility itself, physicians should take the vitamin serum levels under consideration while providing treatment for infertile male patients.