bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optimized protocols for protoplast isolation, transfection, and regeneration in the Solanum genus for the CRISPR/Cas-mediated transgene-free genome editing
Authors: Yang So Hee , Kim Suk Weon , Lee Sujin , Koo Yeonjong 
Published: March 2024

AbstractThe Solanaceae family includes the largest flowering crops such as tomatoes, potatoes, and eggplants. Consumer demand has led to massive development of plants in the Solanum genus, and many different Solanum varieties are now available on the market. The recent advances in Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated protein 9 (Cas9)-based genome editing have allowed laboratories and smaller crop production companies to utilize the technology in various crops. The traditional transformation method in crops involves the use of Agrobacterium, which is considered the most efficient method for introducing exogenous genetic materials in target plants. The Agrobacterium-mediated transformation method has been also established in the Solanaceae family, enabling CRISPR/Cas-based genome editing in crops like tomatoes, potatoes, and eggplants. However, the Agrobacterium-mediated approach inevitably accompanies the insertion of exogenous DNA into the plant genome and often causes the formation of chimera that require further propagation steps. Alternatively, the CRISPR/Cas components can be introduced into protoplasts in the form of DNA for transient expression or a mixture of protein and RNA to avoid genomic insertion of foreign materials. The protoplast transformation approach involves processes including protoplast preparation, transfection, and regeneration, which require a comprehensive understanding and greater technical mastery of the tissue culture phase. Here we highlight the current research advances in protoplast transformation and discuss how to optimize the procedures of protoplast isolation, transfection, and regeneration for efficient and reproducible CRISPR/Cas-based genome editing in the genus Solanum.
Ghosts and teeming worlds
Authors: Bianchetti Cristina 
Published: March 2024

AbstractThe article continues a trajectory of studies performed in the last few years regarding the topic of the body in discourse and urban planning design (Bianchetti. in Bodies between space and design, Jovis, Berlin, 2020, Bianchetti. in “Spazi corpi politiche” dialogue with Simona Forti and Paola Viganò, Biennale Democrazia, Turin, 25 March, Teatro Gobetti, 2023a, Bianchetti. in Le mura di Troia. Lo spazio ricompone i corpi. Donzelli, Rome, 2023b). It takes three books as its focus. The authors are: Colin Rowe and Dennis Hardy, Anthony Vidler, and Antoine Picon. I am personally very attached to these three books and believe they can help understand three different forms of the relationship between spaces and bodies. These forms of the relationship, respectively concern: the recomposition of bodies in space; the transfiguration of space that becomes projection of the neuroses and phobias of those who inhabit it; the tension between materiality and disembodiment. Recomposition, transfiguration, and disembodiment are ways in which spaces and bodies relate to each other. They speak of vulnerability, but also of the power of the body-in-space. The underlying question is: to what extent are urban planning policies and designs able to grasp the irreducibility of bodies? To what extent are they able to overcome the dedifferentiation that has created them for so long? Recomposition, transfiguration and disembodiment force us to reposition our attention beyond the ghost of a pure project, in the fallible and teeming kingdom of the relationships between bodies and spaces. The aim of the article is to highlight fragments of a critical discussion on design based on the complex relations between space, life, bodies and designs.
Blood-based CNS regionally and neuronally enriched extracellular vesicles carrying pTau217 for Alzheimer’s disease diagnosis and differential diagnosis
Authors: Guo Zhen , Tian Chen , Shi Yang , Song Xue-Ru , Yin Wei , Tao Qing-Qing , Liu Jie , Peng Guo-Ping , Wu Zhi-Ying , Wang Yan-Jiang , Zhang Zhen-Xin , Zhang Jing 
Published: March 2024

AbstractAccurate differential diagnosis among various dementias is crucial for effective treatment of Alzheimer’s disease (AD). The study began with searching for novel blood-based neuronal extracellular vesicles (EVs) that are more enriched in the brain regions vulnerable to AD development and progression. With extensive proteomic profiling, GABRD and GPR162 were identified as novel brain regionally enriched plasma EVs markers. The performance of GABRD and GPR162, along with the AD molecule pTau217, was tested using the self-developed and optimized nanoflow cytometry-based technology, which not only detected the positive ratio of EVs but also concurrently presented the corresponding particle size of the EVs, in discovery (n = 310) and validation (n = 213) cohorts. Plasma GABRD+- or GPR162+-carrying pTau217-EVs were significantly reduced in AD compared with healthy control (HC). Additionally, the size distribution of GABRD+- and GPR162+-carrying pTau217-EVs were significantly different between AD and non-AD dementia (NAD). An integrative model, combining age, the number and corresponding size of the distribution of GABRD+- or GPR162+-carrying pTau217-EVs, accurately and sensitively discriminated AD from HC [discovery cohort, area under the curve (AUC) = 0.96; validation cohort, AUC = 0.93] and effectively differentiated AD from NAD (discovery cohort, AUC = 0.91; validation cohort, AUC = 0.90). This study showed that brain regionally enriched neuronal EVs carrying pTau217 in plasma may serve as a robust diagnostic and differential diagnostic tool in both clinical practice and trials for AD.
Combination of a multiplex pneumonia panel and Gram staining for antimicrobial selection to treat lower respiratory tract infection
Authors: Matsuura Hiroshi , Arimoto Koudai , Takahashi Yoshihito , Kishimoto Masafumi 
Published: March 2024

Abstract
Aim
This study aimed to examine the utility of simultaneously performed the Film Array pneumonia panels (pneumonia panels) and Gram staining with the same specimens and evaluate their effect on antimicrobial selection.

Methods
This prospective study, conducted from April 2022 to January 2023, enrolled adult patients with pneumonia, including those with ventilator-associated pneumonia (VAP). Specimens obtained at the time of sputum culture were tested using Gram staining and the pneumonia panel. The patients’ characteristics and pneumonia panel results were assessed. We also evaluated the selection of antimicrobial agents for drug-resistant bacteria detected by the pneumonia panel.

Results
This study comprised 39 patients: 25 patients (64.1%) underwent intubation, including 7 (17.9%) patients with VAP. Most tests were performed at the time of admission, while some were performed during hospitalization. Good quality sputum was obtained from intubated patients. The pneumonia panel detected drug-resistant bacteria in 12 cases. Six patients required antimicrobial escalation, while the antimicrobial regimen remained unchanged for 2 patients in whom Pseudomonas aeruginosa was detected and had already received meropenem. The attending physician did not change the antimicrobials, considering the results of Gram staining and the patient’s general condition in 4 patients.

Conclusions
The pneumonia panel might be useful for detecting drug-resistant organisms at an early stage. It may be important to take the Gram staining results and the patient’s condition into account with pneumonia panel for appropriate antibiotic prescription.
Brand authenticity influence on young adults’ luxury sneakers brand preference: the mediating role of brand image
Authors: Ligaraba Neo , Cheng Joy , Ndungwane Nompumelelo Fortunate , Nyagadza Brighton 
Published: March 2024

AbstractIt is of interest to examine how consumers perceive luxury brands with the different elements of authenticity, leading to brand image, for companies to create and build a brand that is conducive to influence purchase intention. Through a proposed conceptual research model, brand authenticity and brand image as the predictor variables, with brand preference as the outcome variable, the study investigates the causal relationship of these constructs, where eight (8) determinants of brand authenticity are assessed. Findings of the research support all nine proposed hypotheses, as a result, indicated that brand authenticity and brand image influence consumers’ brand preference. The same model development for the current study can be applied in other geographical zones and in different contexts to prove its generalisability. This study assists fashion marketing practitioners and brand managers to remain sustainable and better identify the factors that influence brand authenticity and brand image on brand preference of luxury sneakers among young adults in South Africa. The rapid globalization and increase in competition has caused a shift in the luxury industry so marketers need to focus on the authenticity of a brand to influence consumers’ brand preference. Theoretically, this study adds to the limited academic literature on the theory of reasoned action and the brand equity theory, with regard to branding.
Lithocodium mound identification using logging-while-drilling image log and quantified cutting analysis — Validation with analogues
Authors: Perrin Christian , Pointer Chay , Al-Mohannadi Ghada , Sen Shantanu , Buraimoh Muse Ajadi 
Published: March 2024

Lithocodium mounds are early Cretaceous sedimentary structures described in the literature from outcrops, however, never described in the subsurface. The objective of this work is to identify and characterize Lithocodium mounds in the subsurface along a 25,000 ft horizontal well. Drill cuttings sampled at a 100 ft interval are observed in thin sections to define and quantify key sedimentary indicators (bioclasts, facies, and texture). Logging-while-drilling (LWD) gamma ray (GR), density, neutron, and resistivity logs are acquired along with the LWD high-resolution borehole image (BHI) log. Bedding dips from BHI data, interpreted along the horizontal well, enabled the reconstruction of the reservoir paleotopography. In particular, the alternation of dip azimuth combined with the facies interpretation from the thin sections supported the interpretation of eight distinct mound structures. An assessment of their overall geometry confirmed the mound shape to be subcircular, consistent with the subcircular geometries observed in Oman at the outcrop. The inferred dimensions of the mounds are comparable with the Aptian Lithocodium mounds in Oman (30–40 m), and their intermound organization resembles that of the Albian mounds in Texas. This work demonstrates the value of analyzing cuttings to complement image log interpretation and the value of outcrop analogues for interpreting sedimentary structures. For the first time, the subsurface identification and characterization of Lithocodium mounds and intermounds are achieved.
Development of an Automatic Rule-Based Algorithm for the Detection of Ovarian Cancer Recurrence From Electronic Health Records
Authors: Lee Sanghee , Kim Ji Hyun , Ha Hyeong In , Lim Myong Cheol , Cho Hyunsoon 
Published: March 2024

PURPOSE As the onset of cancer recurrence is not explicitly recorded in the electronic health record (EHR), a high volume of manual chart review is required to detect the cancer recurrence. This study aims to develop an automatic rule-based algorithm for detecting ovarian cancer (OC) recurrence on the basis of minimally preprocessed EHR data. METHODS The automatic rule-based recurrence detection algorithm (Auto-Recur), using notes on image reading (positron emission tomography-computed tomography [PET-CT], CT, magnetic resonance imaging [MRI]), biomarker (CA125), and treatment information (surgery, chemotherapy, radiotherapy), was developed to detect the first OC recurrence. Auto-Recur contains three single algorithms (images, biomarkers, treatments) and hybrid algorithms (combinations of the single algorithms). The performance of Auto-Recur was assessed using sensitivity, specificity, and accuracy of the recurrence time detected. The recurrence-free survival probabilities were estimated and compared with the retrospective chart review results. RESULTS The proposed Auto-Recur considerably reduced human resources and time; it saved approximately 1,340 days when scaled to 100,000 patients compared with the conventional retrospective chart review. The hybrid algorithm on the basis of a combination of image, biomarker, and treatment information was the most efficient (sensitivity: 93.4%, specificity: 97.4%) and precisely captured recurrence time (average time error: 8.5 days). The estimated 3-year recurrence-free survival probability (44%) was close to the estimates by the retrospective chart review (45%, log-rank P value = .894). CONCLUSION Our rule-based algorithm effectively captured the first OC recurrence from large-scale EHR while closely approximating the recurrence-free survival estimates obtained by conventional retrospective chart reviews. The study findings facilitate large-scale EHR analysis, enhancing clinical research opportunities.
Probing Majorana bound states via thermoelectric transport
Authors: Benjamin Colin , Das Ritesh 
Published: March 2024

Abstract
We propose a set of thermoelectric experiments based on Aharonov-Bohm interferometry to probe Majorana bound states (MBS), which are generated in 2D topological insulators (TI) in the presence of superconducting and ferromagnetic correlations via the proximity effect. The existence and nature (coupled or uncoupled) of these MBS can be determined by studying the charge and heat transport, specifically, the behavior of various thermoelectric coefficients like the Seebeck coefficient, Peltier coefficient, thermal conductance, and violations of Wiedemann-Franz law as a function of the Fermi energy and Aharonov-Bohm flux piercing the TI ring with the embedded MBS.
Quantum walk of two non-interacting particles on a 2D lattice
Authors: Han Qi , Bai Ning , Wang Shuai , Gou Lijie , Zhang Rong 
Published: March 2024

Abstract
In this paper, it is sufficient to simply tensor the single-particle unitary operator U
1 for the evolution operator U
2 of two particles that do not have interactions. Subsequently, the operator U
1 is diagonalized and the relative distance between two non-interacting particles on the 2D lattice at the moment t is obtained using the distance evolution operator.
Cechy teksturalne osadów korytowych Wilgi (Polska Południowa) jako odzwierciedlenie zróżnicowania struktury koryta i źródeł dostawy materiału do systemu fluwialnego
Authors: Gołąb Agata , Piątek Dawid , Michno Anna 
Published: March 2024

Wykształcenie i funkcjonowanie koryt rzecznych uwarunkowane jest cechami środowiska przyrodniczego zlewni oraz antropopresją. Uwarunkowania te mają zasadnicze znaczenie w kształtowaniu cech osadów aluwialnych. Głównym celem badań było poznanie zróżnicowania cech teksturalnych współczesnych osadów korytowych Wilgi w nawiązaniu do zróżnicowania struktury jej koryta oraz źródeł dostawy materiału do systemu fluwialnego. Scharakteryzowano strukturę koryta Wilgi ze szczególnym uwzględnieniem rozmieszczenia i cech form akumulacyjnych oraz erozyjnych. Na czterech stanowiskach badawczych, powiązanych z różnymi źródłami dostawy, określono uziarnienie osadów korytowych, ich skład petrograficzny i stopień obróbki. Uzyskane wyniki pokazały zróżnicowanie źródeł dostawy materiału wzdłuż profilu podłużnego koryta. W pogórskim odcinku źródłami dostawy są podcięcia erozji bocznej oraz progi w dnie koryta. Materiał aluwialny w korycie jest ostrokrawędzisty i grubofrakcyjny. W niżej położonej części zlewni, do koryta dostarczany jest materiał drobnoziarnisty budujący szerokie, płaskie dno doliny. Stwierdzono również, że wzdłuż profilu podłużnego koryta największym zmianom ulega uziarnienie oraz stopień obróbki materiału, w mniejszym stopniu skład petrograficzny.
Hasidic Literature Concerning Rationales for the Commandments: Hasidism and Kabbalah in Their Cultural Context
Authors: Sachs-Shmueli Leore , Goldschmidt Roee 
Published: March 2024

Abstract: This article presents a first attempt to classify and present a group of eighteenth- and nineteenth-century Hasidic texts as belonging to a specific literary genre: rationales for the commandments. In this category we include Sefer Toldot Ya‘akov Yosef , by Ya‘akov Yosef of Pollonye; Sefer derekh pikudekhah , by Tsvi Elimelekh of Dinov; Sefer otsar ha-@hayim , by Yits@hak Eizik Ye@hiel Safrin; Likute halakhot , by Nathan Sternharts of Nemirov; Derekh mitsvotekhah , by Menachem Mendel Schneerson; and, finally, Sefer be’erat Miriam , by Avraham Abele Kanarfogel. We survey the works broadly and relate them to one defined literary genre. In so doing, we offer a new framework for a scholarly discussion of the Hasidic occupation with nomos and kabbalah. We demonstrate how Hasidic works discussing rationales for the commandments simultaneously employ halakhic and kabbalistic perspectives, emphasizing the punctiliousness in their fulfilment, their theurgic efficacy, and personal-spiritual completeness.
Dual-comb spectroscopy in the deep ultraviolet
Authors: McCauley John J. , Phillips Mark C. , Weeks Reagan R. D. , Zhang Yu , Harilal Sivanandan S. , Jones R. Jason 
Published: March 2024

This Letter reports dual-frequency-comb spectroscopy in the deep ultraviolet used to characterize transient laser-produced plasmas. Dual-comb spectroscopy at these wavelengths enables access to a large number of strong electronic transitions in neutral and ionized atoms and molecules. This broadband dual-frequency-comb system at 265 nm measures multiple transitions in neutral and singly ionized iron atoms in a laser-produced plasma. Analysis of absorption spectra yields time-resolved ion and neutral column densities, excitation temperatures, and electron densities, which are measured down to 1014cm−3levels. The results provide insights into low-temperature plasma properties.
The Machine Learning Model for Predicting Inadequate Bowel Preparation Before Colonoscopy: A Multicenter Prospective Study
Authors: Gu Feng , Xu Jianing , Du Lina , Liang Hejun , Zhu Jingyi , Lin Lanhui , Ma Lei , He Boyuan , Wei Xinxin , Zhai Huihong 
Published: March 2024

INTRODUCTION:
Colonoscopy is a critical diagnostic tool for colorectal diseases; however, its effectiveness depends on adequate bowel preparation (BP). This study aimed to develop a machine learning predictive model based on Chinese adults for inadequate BP.

METHODS:
A multicenter prospective study was conducted on adult outpatients undergoing colonoscopy from January 2021 to May 2023. Data on patient characteristics, comorbidities, medication use, and BP quality were collected. Logistic regression and 4 machine learning models (support vector machines, decision trees, extreme gradient boosting, and bidirectional projection network) were used to identify risk factors and predict inadequate BP.

RESULTS:
Of 3,217 patients, 21.14% had inadequate BP. The decision trees model demonstrated the best predictive capacity with an area under the receiver operating characteristic curve of 0.80 in the validation cohort. The risk factors at the nodes included body mass index, education grade, use of simethicone, diabetes, age, history of inadequate BP, and longer interval.

DISCUSSION:
The decision trees model we created and the identified risk factors can be used to identify patients at higher risk of inadequate BP before colonoscopy, for whom more polyethylene glycol or auxiliary medication should be used.
Auditor's Reputation and Auditor's Opinion on Stock Prices: Evidence from Indonesia's Main Board Index
Authors: Siagian Valentine 
Published: March 2024

This paper examines the effect of the auditor reputation and the auditor's opinion on the stock prices of the firm in the following year from IndonesiaÂ Main Board Index for the period of 2016 to 2020. This research aims to study the importance of the auditor's reputation and the opinion given to the value of the firm by their stock prices movements in the following year.Â Regression analysis was applied with control variable and year fixed effectÂ to find out whether or not the reputation of the auditor and the opinion givenÂ by the auditor could affect the stock prices of the firm in each sample year.Â The result shows that auditor's reputation does affect the stock prices in theÂ following year which means choosing BIG4 CPA firm will increase stock prices in the following year, while auditor's opinion does not affect the stockÂ prices of the firm in the following year.
Algorithmic Complexity Attacks on Dynamic Learned Indexes
Authors: Yang Rui , Kornaropoulos Evgenios M. , Cheng Yue 
Published: March 2024

Learned Index Structures (LIS) view a sorted index as a model that learns the data distribution, takes a data element key as input, and outputs the predicted position of the key. The original LIS can only handle lookup operations with no support for updates, rendering it impractical to use for typical workloads. To address this limitation, recent studies have focused on designing efficient dynamic learned indexes. ALEX, as the first and one of the representative dynamic learned index structures, enables dynamism by incorporating a series of design choices, including adaptive key space partitioning, dynamic model retraining, and sophisticated engineering and policies that prioritize read/write performance. While these design choices offer improved average-case performance, the emphasis on flexibility and performance increases the attack surface by allowing adversarial behaviors that maximize ALEX's memory space and time complexity in worst-case scenarios.
In this work, we present the first systematic investigation of algorithmic complexity attacks (ACAs) targeting the worst-case scenarios of ALEX. We introduce new ACAs that fall into two categories, space ACAs and time ACAs, which target the memory space and time complexity, respectively. First, our space ACA on data nodes exploits ALEX's gapped array layout and uses Multiple-Choice Knapsack (MCK) to generate an optimal adversarial insertion plan for maximizing the memory consumption at the data node level. Second, our space ACA on internal nodes exploits ALEX's catastrophic cost mitigation mechanism, causing an out-of-memory (OOM) error with only a few hundred adversarial insertions. Third, our time ACA generates pathological insertions to increase the disparity between the actual key distribution and the linear models of data nodes, deteriorating the runtime performance by up to 1, 641× compared to ALEX operating under legitimate workloads.