bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sensitivity analysis of RT-qPCR and RT-ddPCR for SARS-CoV-2 detection with mutations on N1 and E primer-probe region
Authors: Liu Shiyou , Chai Xiaoru , Liu Chao , Bai Jiaxuan , Meng Juntao , Tian Hong , Han Xu , Han Guangyue , Li Qi , Xu Xiangdong 
Published: June 2024

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an RNA virus that undergoes rapid mutation. Based on viral whole genome sequencing analysis in Hebei Province, China, we identified several essential single nucleotide variants (SNVs) on primer-probe regions accumulating within some Omicron variants’ genomes. In this study, we focused on three SNVs, C28290T, T28297C, and C28311T emerging on 2019-nCoV-N1 (CDC-N1) primer-probe regions, recommended by CDC in 2020, and two SNVs, C26270T, A26275G emerging on E (Charité-E) primer-probe regions recommended by Charité, Germany. Our findings revealed that the presence of one or two SNVs in the primer or probe region affected the sensitivity of reverse transcription-quantitative polymerase chain reaction and droplet digital PCR to varying extents. This discovery underscores the importance of continuously monitoring the whole genome sequences of SARS-CoV-2 variants, especially the primer-probe targeting regions, and correspondingly updating commercial test kits or recommended primer-probe sequence sets.

IMPORTANCE
The emergence of new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants has resulted in a growing number of mutations in its genome, presenting new challenges for the diagnosis of SARS-CoV-2 using reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and droplet digital PCR (RT-ddPCR) methods. There is an urgent need to develop refined methods for modifying primers and probes to improve the detection of these emerging variants. In this study, our focus was on the SNVs that have emerged in the CDC-N1 and Charité-E primer-probe regions. Our research has confirmed that the presence of these SNVs in the primer or probe region can significantly affect the results of coronavirus disease 2019 tests. we have developed and validated a modified detection method that can provide higher sensitivity and specificity. This study emphasizes the importance of refining the primer-probe sets to ensure the diagnostic accuracy of RT-qPCR and RT-ddPCR detection.
The Problems of DNA-Barcoding the Shads of Genus Alosa (Alosidae) of the Ponto-Caspian Basin
Authors: Orlova S. Yu. , Emelyanova O. R. , Nebesikhina N. A. , Rabazanov N. I. , Orlov A. M. 
Published: June 2024

Abstract—
Numerous studies show that species identification of representatives of the genus Alosa using various genetic markers is often difficult and the search for more specific biomarkers is required. For the first time we analyzed polymorphism of COI gene fragment of mitochondrial DNA of two representatives of this genus (A. tanaica and A. kessleri), supplemented with new data on A. immaculata, from the waters of the Ponto-Caspian basin in comparative aspect with other representatives of the herring (Clupeoidea) genera Alosa, Clupea, Clupeonella, Sprattus, and Sardinops. The main result was the conclusion that within the genus Alosa, it is not possible to identify species using the marker used. On the one hand, specimens collected from morphologically distinct individuals and identified as different species have the same haplotypes. On the other hand, samples belonging to different species differ from each other by an insignificant number of nucleotide substitutions and do not form independent clades on the phylogram and haplotype network. This indicates the absence of genetic differentiation between the studied samples of herrings of genus Alosa into separate species and species groups when using DNA barcoding based on the COI gene. The reasons for such a phenomenon may be the following: (1) incorrect identification of species in catches, since shads (Alosidae) have high morphological flexibility and in many species, the main external morphological characters often overlap; (2) recent time of speciation by the standards of biological evolution for shads of genus Alosa; (3) difference in proportion of interspecific hybrids, which can vary significantly between populations of the same species.
Impact of a simulated multiday heatwave on nocturnal physiology, behavior, and sleep: a 10-day confinement study
Authors: Ioannou Leonidas G. , Tsoutsoubi Lydia , Mantzios Konstantinos , Ciuha Ursa , Kenny Glen P. , Nybo Lars , Flouris Andreas D. , Mekjavic Igor B. 
Published: June 2024

This study investigated the impact of a multiday heatwave on nocturnal physiology, behavior, and sleep under controlled conditions with comprehensive monitoring of environmental factors and participant activities. Seven young healthy males were confined for 10 days in controlled conditions that ranged between hot-to-warm (day: 35.4 °C, night: 26.3 °C) during nights 4–6 and temperate (day: 25.4 °C, night: 22.3 °C) before (nights 1–3) and after (nights 7–10) the heatwave. Measurements included core and skin temperatures, heart rate, sympathovagal balance, vasomotion indicators, urine samples, blanket coverage, subjective sleep assessments, and partial polysomnography. The average nocturnal core temperature was 0.2 °C higher during and after the heatwave compared to the pre-heatwave period, with this difference being more pronounced (+0.3 °C) in the first 2 h of sleep ( p < 0.001). For every 0.1 °C rise in overnight core temperature, the total sleep time decreased by 14 min (pseudo- R2 = 0.26, p = 0.01). The elevated core temperatures occurred despite the participants exhibiting evident thermoregulatory behavior, as they covered 30% less body surface during the heatwave compared to pre- and post-heatwave periods ( p < 0.001). During the heatwave, mean skin temperature at bedtime was 1.3 °C higher than pre-heatwave and 0.8 °C higher than post-heatwave periods ( p < 0.001). No differences in other responses, including heart rate and vasomotion indicators, were observed. The paper details a 20-min sleepwalking episode that was coupled with marked changes in sleepwalker’s thermophysiological responses. In conclusion, the simulated heatwave resulted in higher overnight core temperature which was associated with reduced total sleep time. Behavioral thermoregulation during sleep may serve as a defense against these effects, though more research is needed.
Intriguing properties of transport at the microscales: Langevin equation approach
Authors: Spiechowicz J. , Łuczka J. 
Published: June 2024

Abstract
We present a perspective of simple models of nonequilibrium directed transport described in terms of a Langevin equation formalism. We consider a Brownian particle under various circumstances and driven by thermal (equilibrium) and non-thermal (active) fluctuations. Three examples of startling behavior are unveiled: giant transport, multiple current reversal and negative mobility.

Abstract

Graphic abstract
Timelike bound orbits and pericenter precession around black hole with conformally coupled scalar hair
Authors: Qi Qi , Kuang Xiao-Mei , Li Yong-Zhuang , Sang Yu 
Published: June 2024

AbstractWe investigate the geodesic motions of timelike particles around a static hairy black hole with conformally coupled scalar field. We mainly focus on the effects of the scalar charge and electric charge on the marginally bound orbits (MBO), innermost stable circular orbits (ISCO) and on the precessing orbits around this black hole. Our results show that both the scalar and electric charges suppress the energy as well as the angular momentum of the particles in the bound orbits. Then, we study the relativistic periastron precessions of the particles and constrain the charge parameters by employing the observational result of the S2 star’s precession in SgrA*. It is found that the constraints on the charge parameters from S2 star’s motion are tighter than those from black hole shadow. Finally, we analyze the periodic motions of the particles and figure out samples of periodic orbits’ configurations around the hairy black hole.
Case 326: Intra-Articular Osteoid Osteoma
Authors: Iwasaka-Neder Jade , Bedoya M. Alejandra , Tsai Andy , Bixby Sarah D. 
Published: June 2024

History A 15-year-old male patient presented with a 3-week history of inner left thigh pain provoked by activity and experienced occasionally at rest. The patient denied nighttime pain, fever, or chills. Laboratory investigation revealed the following normal values: hemoglobin level of 15.6 g/dL (normal range, 13–16 g/dL), platelet count of 240 × 103/µL (normal range, 140–440 × 103/µL), and total leukocyte count of 7100 cells/µL (normal range, 4500–11 000 cells/µL). The percentage of neutrophils was considered low at 44% (normal range, 54%–62%), and the percentage of eosinophils was slightly high at 3.7% (normal range, 0%–3%). An anteroposterior radiograph of the left hip is shown. Physical therapy was initiated, with no improvement after 2 weeks of therapy. The patient was referred to an orthopedist for further evaluation. At physical examination, the patient endorsed marked left hip pain with hip flexion to 90°, limited internal and external rotation (5° and 15°, respectively), and antalgic gait favoring the left leg. Hip MRI and further serologic analysis were requested for further evaluation. Although the serologic testing was performed at an outside laboratory, the physician reported positive immunoglobulin-G Lyme titers, normal C-reactive protein level, and normal erythrocyte sedimentation rate. Pelvic CT was requested. The patient was prescribed a course of doxycycline (100 mg twice daily for 28 days), with reported resolution of symptoms 2 weeks after initiation of treatment. Three weeks later, the patient presented to our department with recurrent left hip pain, which was similar in severity compared with the initial presentation. A second MRI examination of the left hip was performed 4 months after the initial presentation.
TGFβ in Pancreas and Colorectal Cancer: Opportunities to Overcome Therapeutic Resistance
Authors: Johansen Allan M. , Forsythe Steven D. , McGrath Callum T. , Barker Grayson , Jimenez Hugo , Paluri Ravi K. , Pasche Boris C. 
Published: June 2024

Abstract
TGFβ is a pleiotropic signaling pathway that plays a pivotal role in regulating a multitude of cellular functions. TGFβ has a dual role in cell regulation where it induces growth inhibition and cell death; however, it can switch to a growth-promoting state under cancerous conditions. TGFβ is upregulated in colorectal cancer and pancreatic cancer, altering the tumor microenvironment and immune system and promoting a mesenchymal state. The upregulation of TGFβ in certain cancers leads to resistance to immunotherapy, and attempts to inhibit TGFβ expression have led to reduced therapeutic resistance when combined with chemotherapy and immunotherapy. Here, we review the current TGFβ inhibitor drugs in clinical trials for pancreatic and colorectal cancer, with the goal of uncovering advances in improving clinical efficacy for TGFβ combinational treatments in patients. Furthermore, we discuss the relevance of alterations in TGFβ signaling and germline variants in the context of personalizing treatment for patients who show lack of response to current therapeutics.
Exploration of Immune-Modulatory Effects of Amivantamab in Combination with Pembrolizumab in Lung and Head and Neck Squamous Cell Carcinoma
Authors: Lim Sun M. , Kang Seong-san , Kim Dong K. , Lee Soo-Hwan , Synn Chun-Bong , Baek Sujeong , Yang Seung M. , Han Yu J. , Kim Mi H. , Han Heekyung , Na Kwangmin , Kim Young T. , Yun Mi R. , Kim Jae H. , Byeon Youngseon , Kim Young S. , Lee Jii B. , Hong Min H. , Curtin Joshua C. , Patel Bharvin , Bergiers Isabelle , Pyo Kyoung-Ho , Cho Byoung C. 
Published: June 2024

Abstract

Immune checkpoint inhibitors are effective first-line therapy for solid cancers. However, low response rate and acquired resistance over time has led to the need for additional therapeutic options. Here, we evaluated synergistic antitumor efficacy of EGFR × MET targeting bispecific antibody, amivantamab with PD-L1 immunotherapy, pembrolizumab in head and neck squamous cell carcinoma (HNSCC) and lung squamous cell carcinoma tumor–bearing humanized patient-derived xenograft (PDX) models. We demonstrated that pembrolizumab or amivantamab alone was ineffective and that combination treatment induced a significant reduction of tumor growth in both models (P &lt; 0.0001 and P &lt; 0.01, respectively). It appeared that combination of amivantamab and pembrolizumab significantly enhanced infiltration of granzyme B–producing CD8 T cells was in the TME of HNSCC PDX (P &lt; 0.01) and enhanced neoantigen-associated central memory CD8 T cells in circulating immune cells. Analysis of single-cell RNA transcriptomics suggested that the tumor cells dramatically upregulated EGFR and MET in response to PD-L1 immunotherapy, potentially creating a metabolic state fit for tumor persistence in the tumor microenvironment (TME) and rendered pembrolizumab ineffective. We demonstrated that EGFRHIGHMETHIGH subcluster displayed an increased expression of genes implicated in production of lactate [SLC16A3 and lactate dehydrogenase A (LDHA)] compared to the EGFRLOWMETLOW cluster. Accumulation of lactate in the TME has been associated with immunosuppression by hindering the infiltration of tumor killing CD8 T and NK cells. This study proved that amivantamab reduced glycolytic markers in the EGFRHIGHMETHIGH subcluster including SLC16A3 and LDHA and highlighted remodeling of the TME by combination treatment, providing rationale for additional therapy of amivantamab with PD-1 immunotherapy.

Significance:
Amivantamab in synergy with pembrolizumab effectively eradicated EGFRHIGHMETHIGH tumor subcluster in the tumor microenvironment of head and neck squamous cell carcinoma and overcame resistance against anti-PD-1 immunotherapy.
Advanced image stitching method and evaluation for underwater structure inspection utilizing planar array cameras
Authors: Hou Shitong , Wang Yuxuan , Wu Gang , Wu Tao , Wang Shunyao , Jiang Hejun , Fan Xiao , Zhang Yujie 
Published: June 2024

The inspection of underwater structural health is crucial for comprehensive bridge health assessments. In underwater structure imaging, traditional methods include single-camera and binocular camera inspection. However, due to water turbidity and long working distances with a small field-of-view, obtaining clear and high-quality detection images with these methods takes much work. To address this problem, this paper presents a method for planar array image stitching based on Harris corner point extraction, utilizing the advantages of planar array cameras characterized by short working distances and wide field-of-view. The core contribution of this paper is the introduction of an innovative image sequence stitching algorithm utilizing Harris corner point extraction and the combination of the first proposed planar array cameras with the image sequence stitching algorithm, which solves the problem of long distance and small field-of-view during the underwater inspection. The image stitching method involves calibrating camera parameters with a checkerboard and stitching underwater images from planar array cameras to reveal underwater structural features. Furthermore, five quantitative evaluation metrics and the method for calculating the field-of-view loss rate are presented to evaluate and analyze the stitched images. A series of experiments were performed on concrete surfaces, aquatic and underwater, with a total field-of-view of the underwater image after stitching of 358.86 mm × 319.24 mm at a working distance of 160 mm. Five evaluation methods were used to quantitatively evaluate the quality of the stitched images and calculate the field-of-view loss rate of the images. The results indicate that the proposed method improves the ability to inspect underwater. The stitched images achieve notable metrics: an entropy of approximately 6.7, an average gradient of about 1.7, a spatial frequency of around 3.5, an edge strength of about 17, mutual information of approximately 1.2, and a field-of-view loss rate of <0.1, facilitating more effective underwater structure inspection.
Mirror artefact as a diagnostic tool in identifying occult liver lesions on ultrasound
Authors: Wang Yi (Elaine) , Najafzadeh Abriz Afrooz 
Published: June 2024

Introduction: Mirror artefacts often can be seen in abdominal ultrasound. Their efficacy in detecting sonographically occult lesions has been overlooked. Case report: We present two cases of abdominal ultrasound examination, where the mirror image artefact was utilised in the diagnosis of sonographically occult lesions in segment VII of the liver. Discussion: The physical principle behind the mirror image artefacts in these cases has been explored and explained. Suggestion on utilising this artefact is recommended. Conclusion: These cases demonstrate the key role that mirror artefacts played in detecting occult liver lesions. Sonographers are advised to extend their survey of the right liver and pay close attention to displayed mirror images above the diaphragm especially from potential sonographically occult lesions in segment VII of the liver.
Clot migration in patients treated with tenecteplase versus alteplase before mechanical thrombectomy
Authors: García-Alcántara Gabriel , Moreno-López Cristina , López-Rebolledo Rodrigo , Lorenzo-Barreto Pablo , Garay-Albízuri Patricia , Martínez-García Beatriz , Llanes Ana , Pérez-Gil Daniel , Chico Juan Luis , Vera-Lechuga Rocío , García-Madrona Sebastián , Matute-Lozano Consuelo , De Felipe-Mimbrera Alicia , Masjuan Jaime , Cruz-Culebras Antonio 
Published: June 2024

Introduction: This study aimed to describe and analyze the rate of clot migration of vessel thrombosis to distal segments in patients with acute ischemic stroke (AIS) who received intravenous thrombolysis (IVT) with tenecteplase (TNK) and alteplase (ALT) before mechanical thrombectomy (MT). In addition, we aimed to determine the relationship between thrombus migration and functional prognosis. Methods: This study followed the STROBE reporting guidelines. We performed a retrospective analysis of a series of patients from November 2017 to April 2023 with an AIS with thrombosis on CT imaging, treated with IVT (TNK or ALT, split into two distinct groups) prior to mechanical thrombectomy. Results: Two hundred and fifty-six patients with large vessel occlusion (LVO) were included. Ninety-six had received TNK. One hundred and sixty had received ALT. Of the 96 TNK patients, 25 experienced either complete recanalization ( n = 3) or thrombus migration ( n = 22). Of the 160 ALT patients, 20 experienced either complete recanalization ( n = 6) or thrombus migration ( n = 14). The difference being statistically substantial for the thrombus migration rate (OR = 3.61, 95% confidence interval: 1.63; 7.98). Migration to an irretrievable very distal segment occurred in four (4%) patients with TNK and in three patients (2%) with ALT ( p > 0.05). Thrombus migration was not significantly associated to a different functional prognosis, measured through Rankin scale after 3 months (OR = 0.44, 95% confidence interval: 0.17; 1.12). Conclusion: The use of TNK over ALT as a fibrinolytic agent is associated with a higher thrombus migration rate. The migration of thrombi to distal segments, which are theoretically less accessible for mechanical thrombectomy, did not result in worse clinical outcomes.
Atrial fibrillation and short-term outcomes after cancer-related ischemic stroke
Authors: Wahbeh Farah , Zhang Cenai , Beyeler Morin , Kaiser Jed H , Liao Vanessa , Pawar Anokhi , Kamel Hooman , Navi Babak B 
Published: June 2024

Introduction: Atrial fibrillation (AF) and cancer are each associated with worse outcomes in patients with acute ischemic stroke (AIS). Few studies have evaluated the impact of AF on outcomes of cancer-related stroke. Patients and methods: We conducted a retrospective cross-sectional study using the 2016–2019 National Inpatient Sample, identifying all hospitalizations with diagnosis codes for cancer and AIS. The primary exposure was a diagnosis of AF. The primary outcome was in-hospital mortality. The secondary outcomes were length-of-stay and discharge to non-home locations. We used multiple logistic and linear regression models, adjusted for age, gender, race-ethnicity, and the Charlson Comorbidity Index, to examine the association between AF and study outcomes. Results: Among 150,200 hospitalizations with diagnoses of cancer and AIS (mean age 72 years, 53% male), 40,084 (26.7%) included comorbid AF. Compared to hospitalizations without AF, hospitalizations with AF had higher rates of in-hospital mortality (14.8% [95% CI, 14.0%−15.6%] vs 12.1% [95% CI, 11.6%−12.5%]) and non-home discharge disposition (83.5% [95% CI, 82.7%−84.3%] vs 75.1% [95% CI, 74.5%−75.7%]) as well as longer mean length-of-stay (8.4 days [95% CI, 8.2–8.6 days] vs 8.2 days [95% CI, 8.0–8.3 days]). In multivariable analyses, AF remained independently associated with higher odds of in-hospital mortality (adjusted odds ratio [aOR], 1.34; 95% CI, 1.24–1.46), non-home discharge disposition (aOR, 1.32; 95% CI, 1.23–1.42), and longer length-of-stay (adjusted mean difference, 13.7%; 95% CI, 10.9%−16.7%). Discussion and conclusion: In cancer-related AIS, comorbid AF is associated with worse short-term outcomes, including higher odds for in-hospital mortality, poor discharge disposition, and longer hospital stays.