bluuebunny/crossref_metadata_2025 huggingface dataset:
Evaluation of Kappa‐carrageenan supplementation in extender for post‐thaw Kajli ram sperm quality
Authors: Qadeer Saima , Ashraf Asma , Farooq Muhammad Umer , Ullah Sana , Asad Muhammad , Muneeb Ahmad , Adil Muhammad
Published: March 2024

Cryopreservation is one of the reliable techniques for long‐term storage of sperm. The success of this technique depends on the choice of cryoprotectant; therefore, a plethora of literature has reported the effects of different cryoprotective agents so far. Kappa‐carrageenan (κ‐carrageenan) is a hydrocolloid polysaccharide extracted from red marine seaweed. Its unique property makes it a promising option as a non‐colligative cryoprotectant. The current study aims to evaluate the cryoprotective effect of k‐carrageenan along with glycerol on ram sperm quality both after equilibration and freezing. Nine Kajli rams were utilized in this experiment for semen collection through an artificial vagina maintained at 42°C. Qualified samples were diluted in tris egg yolk glycerol (TEYG) extender containing different concentrations of k‐carrageenan as 0 mg/mL (control), 0.2, 0.5, 0.8 and 1 mg/mL. Post‐thaw assessment was done at 37°C after 24 h of storage, which showed a significant improvement (p < .05) in sperm viability, motility, membrane and acrosome integrity in an extender containing k‐carrageenan at a concentration of 0.5 mg/mL compared to control. It is concluded from the current study that the combination of glycerol and 0.5 mg/mL concentration of k‐carrageenan improved the sperm post‐thaw quality.
Unofficial intermediation in the regulatory governance of hazardous chemicals
Authors: Hysing Erik , Du Rietz Dahlström Sabina
Published: March 2024

Regulatory intermediaries—organizations that operate between regulators (public and private) and target groups—perform a range of important functions. While most previous research has focused on intermediaries that have been delegated official authority, in this paper we focus on unofficial and informal intermediary functions aiming to advance the governance of per‐ and polyfluoroalkyl substances (PFAS) chemicals. Chemical pollution is a growing environmental and health concern, leading to both public and private regulatory initiatives. By studying a particular segment—paperboard food packaging in Sweden—the study generates insights into critical functions performed by unofficial intermediaries (Svenskt Vatten and ChemSec) in this regulatory regime, which extend and expand regulatory reach in various ways. The study also shows the importance of different types of intermediaries that interact in dynamic ways, and the role of material artifacts in processes of intermediation. These unofficial functions are arguably important for the functioning of complex, hybrid forms of governance, but they also prompt critical questions about the effectiveness, legitimacy, and role of intermediaries in generating needed transformative change.
Processing Large‐Scale Archival Records: The Case of the Swiss Parliamentary Records
Authors: Salamanca Luis , Brandenberger Laurence , Gasser Lilian , Schlosser Sophia , Balode Marta , Jung Vincent , Perez‐Cruz Fernando , Schweitzer Frank
Published: March 2024

Legislative bodies generally keep records of their activities. While the digitization wave spurred the availability of archival documents, their processing remains a challenge. The Swiss parliamentary records are no exception.

In this paper we present a supervised pipeline for extracting and structuring of content of archival records. Our pipeline consists of five steps, starting with an assessment of which elements need extraction and how they relate to each other. Step two involves general pre‐processing to prepare the PDF documents and is followed by an element classification step. Step four involves post‐processing and the final step is a validation of the extracted information. With our supervised approach, we are able to process over 200,000 pages of Swiss parliamentary records (spanning the years 1891–1995), a feat that would exceed the budget of most projects using manual curation. We discuss validation of individual steps and offer guidance to researchers engaged in similar data processing efforts.
An economy of immunity: The racial‐spatial lives of antibodies in the American blood plasma economy from 1960s prisons to COVID‐19
Authors: Johnson Kelsey
Published: March 2024

In 2020, a market in convalescent blood plasma developed as a potential treatment for COVID‐19. During this time, commercial plasma centres—which collect the blood plasma from paid donors for pharmaceutical production—paid recovered patients as much as US$100 for a donation of blood plasma containing COVID‐19 antibodies, from which they manufactured an experimental treatment. This paper uses the commercial collection of COVID‐19 antibodies found in plasma as an entry point into exploring how racially uneven exposures to disease may produce biovalue. The first section considers the spatial history of antibody‐derived plasma products, using historical research to examine how inmates at predominantly black plantation‐prisons in the US South were valued for antibody production in the 1960s. Against this historical relief, the second section examines the spatiality of antibodies in current practices of the plasma industry, as well as in the plasma industry's response to the COVID‐19 pandemic (even as those efforts eventually failed in clinical trials). If geographical literatures on environmental exposure, as well as on COVID‐19 transmission, discuss exposure as an outcome of racial capitalism, this paper emphasises the productive opportunities that capital can solicit from exposures, especially those that are useful to different forms of biomedicine. By critically scrutinising the practice of ‘sharing immunity’ and attending to its decidedly geographic constitution, we can see how what Ruth Wilson Gilmore calls the ‘death‐dealing logics’ of racial capitalism may also work through the seemingly affirmative practices and communal imaginaries behind the redistribution of antibodies as medicine.
Effects of an Annular Baffle on Heat Transfer to an Immersed Coil Heat Exchanger in Thermally Stratified Tanks
Authors: Nicodemus Julia , Smith Joshua , Noreika Joseph , Gomi Manaka , Zhou Tingyu
Published: March 2024

The effect of a cylindrical baffle on heat transfer to an immersed heat exchanger is investigated in initially thermally stratified tanks. The heat exchanger is located in the annular region created by the baffle and the tank wall. Three different cases of initial thermal stratification are explored, and in each case, experiments are conducted with and without the baffle in the stratified tank and in a comparable isothermal tank with the same initial energy, enabling exploration of the role of the baffle in a stratified tank and the role of stratification in tanks with or without the baffle. The baffle maintains the high initial temperature of the upper zone of the stratified tank for 10–16 min, as cool plumes that form on the heat exchanger are confined to the annular baffle region until they exit at the bottom of the tank. Regardless of stratification, the baffle always improves heat transfer to the immersed heat exchanger. In the isothermal tanks, the baffle increases total energy extracted in the first 30 min of discharge by over 20%. In stratified tanks, the baffle increases total energy extracted in 30 min of discharge by 9–16%. Initially, improvement in heat transfer in stratified tanks is due to the higher driving temperature differences around the heat exchanger. Later, after all the water from the hot zone has entered and flowed through the baffle, the tank is basically isothermal, and velocity increases as the fluid temperature drops, maintaining rates of heat transfer higher than that in the tank without the baffle. Stratification improves heat transfer in tanks without a baffle because, by design, the driving temperature difference between the heat exchanger wall and the surrounding fluid is considerably higher. However, in tanks with the baffle, stratification has only a modest positive effect on heat transfer to the immersed heat exchanger.
Epidemiology of Shoulder Dislocations Presenting to Emergency Departments in the United States, 2007–2020
Authors: Rodriguez Rebecca R. , Lam Kenneth C.
Published: March 2024

Context: Shoulder dislocations are the most commonly treated joint dislocation in the emergency department. Zacchilli and Owens previously reported on the epidemiology of shoulder dislocations presenting to the emergency department in the United States from 2002 to 2006. At the time of data collection and analysis, no epidemiological report had been published to update these findings. Purpose: The purpose of our study was to provide an updated epidemiological report from 2007 to 2020. Results: A total of 26,203 shoulder dislocations were recorded in the National Electronic Injury Surveillance System database from 2007 to 2020. The highest rates occurred in males (71.4%, n = 18,722) and patients aged 20–29 years old (28.2%, n = 7,292). The most common mechanism of injury was sports involvement (48.6%, n = 12,735). Interpretation: Our findings suggest that rates of shoulder dislocations have remained consistent with previous research on this topic, indicating no significant changes over the past 19 years. More effective prevention strategies are needed, especially for at-risk populations.
Recent H9N2 avian influenza virus lost hemagglutination activity due to a K141N substitution in hemagglutinin
Authors: Wen Feng , Yan Zhanfei , Chen Gaojie , Chen Yao , Wang Nina , Li Zhili , Guo Jinyue , Yu Hai , Liu Quan , Huang Shujian
Published: March 2024

The H9N2 avian influenza virus (AIV) represents a significant risk to both the poultry industry and public health. Our surveillance efforts in China have revealed a growing trend of recent H9N2 AIV strains exhibiting a loss of hemagglutination activity at 37°C, posing challenges to detection and monitoring protocols. This study identified a single K141N substitution in the hemagglutinin (HA) glycoprotein as the culprit behind this diminished hemagglutination activity. The study evaluated the evolutionary dynamics of residue HA141 and studied the impact of the N141K substitution on aspects such as virus growth, thermostability, receptor-binding properties, and antigenic properties. Our findings indicate a polymorphism at residue 141, with the N variant becoming increasingly prevalent in recent Chinese H9N2 isolates. Although both wild-type and N141K mutant strains exclusively target α,2-6 sialic acid receptors, the N141K mutation notably impedes the virus’s ability to bind to these receptors. Despite the mutation exerting minimal influence on viral titers, antigenicity, and pathogenicity in chicken embryos, it significantly enhances viral thermostability and reduces plaque size on Madin-Darby canine kidney (MDCK) cells. Additionally, the N141K mutation leads to decreased expression levels of HA protein in both MDCK cells and eggs. These findings highlight the critical role of the K141N substitution in altering the hemagglutination characteristics of recent H9N2 AIV strains under elevated temperatures. This emphasizes the need for ongoing surveillance and genetic analysis of circulating H9N2 AIV strains to develop effective control and prevention measures.

IMPORTANCE

The H9N2 subtype of avian influenza virus (AIV) is currently the most prevalent low-pathogenicity AIV circulating in domestic poultry globally. Recently, there has been an emerging trend of H9N2 AIV strains acquiring increased affinity for human-type receptors and even losing their ability to bind to avian-type receptors, which raises concerns about their pandemic potential. In China, there has been a growing number of H9N2 AIV strains that have lost their ability to agglutinate chicken red blood cells, leading to false-negative results during surveillance efforts. In this study, we identified a K141N mutation in the HA protein of H9N2 AIV to be responsible for the loss of hemagglutination activity. This finding provides insight into the development of effective surveillance, prevention, and control strategies to mitigate the threat posed by H9N2 AIV to both animal and human health.
Potent small molecule inhibitors against the 3C protease of foot-and-mouth disease virus
Authors: Kim Yunjeong , Pool Emma , Kim Eunji , Dampalla Chamandi S. , Nguyen Harry Nhat , Johnson David K. , Lovell Scott , Groutas William C. , Chang Kyeong-Ok
Published: March 2024

Foot-and-mouth disease (FMD) is one of the most devastating diseases of livestock which can cause significant economic losses, especially when introduced to FMD-free countries. FMD virus (FMDV) belongs to the family
Picornaviridae
and is antigenically heterogeneous with seven established serotypes. The prevailing preventive and control strategies are limited to restriction of animal movement and elimination of infected or exposed animals, which can be potentially combined with vaccination. However, FMD vaccination has limitations including delayed protection and lack of cross-protection against different serotypes. Recently, antiviral drug use for FMD outbreaks has increasingly been recognized as a potential tool to augment the existing early response strategies, but limited research has been reported on potential antiviral compounds for FMDV. FMDV 3C protease (3Cpro) cleaves the viral-encoded polyprotein into mature and functional proteins during viral replication. The essential role of viral 3Cpro in viral replication and the high conservation of 3Cpro among different FMDV serotypes make it an excellent target for antiviral drug development. We have previously reported multiple series of inhibitors against picornavirus 3Cpro or 3C-like proteases (3CLpros) encoded by coronaviruses or caliciviruses. In this study, we conducted structure-activity relationship studies for our in-house focused compound library containing 3Cpro or 3CLpro inhibitors against FMDV 3Cpro using enzyme and cell-based assays. Herein, we report the discovery of aldehyde and α-ketoamide inhibitors of FMDV 3Cpro with high potency. These data inform future preclinical studies that are related to the advancement of these compounds further along the drug development pathway.

IMPORTANCE

Food-and-mouth disease (FMD) virus (FMDV) causes devastating disease in cloven-hoofed animals with a significant economic impact. Emergency response to FMD outbreaks to limit FMD spread is critical, and the use of antivirals may overcome the limitations of existing control measures by providing immediate protection for susceptible animals. FMDV encodes 3C protease (3Cpro), which is essential for virus replication and an attractive target for antiviral drug discovery. Here, we report a structure-activity relationship study on multiple series of protease inhibitors and identified potent inhibitors of FMDV 3Cpro. Our results suggest that these compounds have the potential for further development as FMD antivirals.
Determination of the cycle threshold value of the Xpert Xpress SARS-CoV-2/Flu/RSV test that corresponds to the presence of infectious SARS-CoV-2 in anterior nasal swabs
Authors: Relich Ryan F. , Van Benten Kayla , Lei Guang-Sheng , Robinson Christopher M. , Carozza Mariel , Sahoo Malaya K. , Huang ChunHong , Solis Daniel , Sibai Mamdouh , Myers Christopher A. , Sikorski Cynthia , Balagot Caroline , Yang David , Pinsky Benjamin A. , Loeffelholz Michael J.
Published: March 2024

Despite having high analytical sensitivities and specificities, qualitative SARS-CoV-2 nucleic acid amplification tests (NAATs) cannot distinguish infectious from non-infectious virus in clinical samples. In this study, we determined the highest cycle threshold (Ct) value of the SARS-CoV-2 targets in the Xpert Xpress SARS-CoV-2/Flu/RSV (Xpert 4plex) test that corresponded to the presence of detectable infectious SARS-CoV-2 in anterior nasal swab samples. A total of 111 individuals with nasopharyngeal swab specimens that were initially tested by the Xpert Xpress SARS-CoV-2 test were enrolled. A healthcare worker subsequently collected anterior nasal swabs from all SARS-CoV-2-positive individuals, and those specimens were tested by the Xpert 4plex test, viral culture, and laboratory-developed assays for SARS-CoV-2 replication intermediates. SARS-CoV-2 Ct values from the Xpert 4plex test were correlated with data from culture and replication intermediate testing to determine the Xpert 4plex assay Ct value that corresponded to the presence of infectious virus. Ninety-eight of the 111 (88.3%) individuals initially tested positive by the Xpert Xpress SARS-CoV-2 test. An anterior nasal swab specimen collected from positive individuals a median of 2 days later (range, 0–9 days) tested positive for SARS-CoV-2 by the Xpert 4plex test in 39.8% (39/98) of cases. Of these samples, 13 (33.3%) were considered to contain infectious virus based on the presence of cultivable virus and replication intermediates, and the highest Ct value observed for the Xpert 4plex test in these instances was 26.3. Specimens that yielded Ct values of ≤26.3 when tested by the Xpert 4plex test had a likelihood of containing infectious SARS-CoV-2; however, no infectious virus was detected in specimens with higher Ct values.

IMPORTANCE

Understanding the correlation between real-time PCR test results and the presence of infectious SARS-CoV-2 may be useful for informing patient management and workforce return-to-work or -duty. Further studies in different patient populations are needed to correlate Ct values or other biomarkers of viral replication along with the presence of infectious virus in clinical samples.
Granular Aluminum Kinetic Inductance Nonlinearity
Authors: Zhdanova M. , Pologov I. , Svyatsky G. , Chichkov V. , Maleeva N.
Published: March 2024

Granular Aluminum is a superconductor known for more than eighty years, which recently found its ap-plication in qubits, microwave detectors and compact resonators, due to its high kinetic inductance, critical magnetic field and critical current. Here we report on the nonlinear dependence of granular Aluminum inductance on current, which hints towards parametric amplification of the microwave signal in granular Aluminum films. The phase shift of the microwave signal reached 4 rad at a frequency of 7 GHz, which makes it possible to estimate the nonlinearity of the system as $$\Delta \phi {\text{/}}\phi = 1.4{\kern 1pt} \% $$ and the potential gain of the order of 17 dB.
Gravitationally induced unified relation among duality, coherence, steering, and maximal average fidelity
Authors: Chen Duo-Duo , Dong Dong-Dong , Song Xue-Ke , Ye Liu , Wang Dong
Published: March 2024

Recently, numerous measures have been proposed for quantifying the quantumness of a given system, and the existence of intrinsic connections among quantum resource measures has been proven. Here, we study the unified relationship between duality, first-order coherence, three-setting linear steering inequality, and maximum average fidelity between two masses due to gravity. Under gravitational inducement, an equivalent relationship was identified between the first-order coherence and duality. The coherence of a system can be controlled by adjusting arm lengths and the distance between the arms of an interferometer. In most cases, the first-order coherence of a system cannot be maximised. Furthermore, a trade-off relationship between gravitationally induced duality and steering violations was derived. We can adjust the arm length and distance between the arms of the interferometer such that the steering violation reaches its maximum at phase $$\pi $$
π
. The results show that the value of the steering violation is always greater than 1; that is, the state of the system is steerable. In addition, we explored the intrinsic relationship between duality and the maximal average fidelity due to gravity. In most cases, the maximum average fidelity of the system is greater than 2/3, indicating that the state is useful for quantum teleportation. These results are important for investigating the intrinsic relationships among various quantum resources within the framework of gravity.
Electron EDM and LFV decays in the light of Muon $$(g-2)_\mu $$ with U(2) flavor symmetry
Authors: Tanimoto Morimitsu , Yamamoto Kei
Published: March 2024

We study the interplay of New Physics (NP) among the lepton magnetic moment, the lepton flavor violation (LFV) and the electron electric dipole moment (EDM) in light of recent data of the muon$$(g-2)_\mu $$(g-2)μ. The NP is discussed in the leptonic dipole operator with theU(2) flavor symmetry of the charged leptons, where possible CP violating phases of the three family space are taken into account. It is remarked that the third-family contributes significantly to the LFV decay,$$\mu \rightarrow e\gamma $$μ→eγ, and the electron EDM. The experimental upper-bound on$$\mu \rightarrow e\gamma $$μ→eγdecay gives a severe constraint on the parameters of the flavor model. The predicted electron EDM is rather large due to the CP violating phases in the three family space. In addition, we also study$$(g-2)_{e,\tau }$$(g-2)e,τof the electron and tauon, and EDMs of the muon and tauon as well as the$$\tau \rightarrow e \gamma $$τ→eγand$$\tau \rightarrow \mu \gamma $$τ→μγdecays. The$$\tau _R \rightarrow \mu _L \gamma $$τR→μLγdecay is predicted to be close to the experimental upper-bound.
The spin-5/2 Blume–Capel model by mean-field approach and renormalization group theory
Authors: Badrour I. A. , Aharrouch R. , Hachem N. , Al-Rajhi A. , El Bouziani M.
Published: March 2024

The spin-5/2 Blume–Capel model was studied using the mean-field approximation and the Migdal–Kadanoff renormalization group method for two- and three-dimensional systems. We determined the phase diagrams in the (crystal field, temperature) plane where the system exhibited first- and second-order phase transitions as well as isolated critical, bicritical and triple points. In order to show first-order transitions at low temperature, we presented the total magnetization per site and the derivative of the free energy as a function of the crystal field. Moreover, the critical exponents of the system were calculated by linearizing the renormalization transformation at the vicinity of the second-order fixed points.
Tuning the electro-optical properties of germanene nanoribbons by boron atom substitution for application in information transmission
Authors: Ngoc Hoang Van , Ha Chu Viet
Published: March 2024

Germanene nanoribbons, a one-dimensional material, have great potential for future technological applications. This research aims to investigate the electro-optical properties of boron-doped germanene nanoribbons with a width of five atoms. The theory used in this study is density functional theory (DFT). The original system is a narrow band gap semiconductor, with a gap size of 0.06[Formula: see text]eV. The doped configurations, which retain the honeycomb hexagonal structure, are stable and metallic in nature. The introduction of B atoms flattens the configuration, leading to a partial charge shift from Ge to B. The absorption peaks in the 3B and 5B configurations occur in the frequency range less than 500[Formula: see text]nm, indicating good absorption of visible light, and suggesting possible applications in light-sensitive components. Notably, the real part of the dielectric function’s 0z component is negative, offering immense potential for optical, microwave and communication applications.
Chemical reaction effect across the moving flat plate with heat generation and MHD flow of Maxwell fluid with viscous dissipation
Authors: Sudarmozhi K. , Iranian D. , Khan Ilyas
Published: March 2024

In this paper, the investigation centered on examining a Maxwell fluid’s convective double diffusive flow carefully considers factors such as chemical reactions, radiation, and the presence of a permeable moving flat plate. Additionally, the study encompassed the effects of heat generation and magnetohydrodynamics (MHD). The governing equations, initially expressed as partial differential equations, were converted into ordinary differential equations using a similarity transformation technique to facilitate the analysis. The computational power of MATLAB’s BVP4C software was harnessed to solve this resultant system of ODEs efficiently. The outcomes of this investigation were presented in the form of graphical representations that vividly depicted the behavior of the flow field, energy conservation, and concentration profiles under various parameter combinations. The research findings were thoughtfully summarized in a table, offering a comprehensive overview of temperature, velocity, and mass profiles across various parameters. These parameters included the Deborah number, chemical reaction rate, Eckert number, Lewis number, Prandtl number, porosity parameter, and MHD parameter. A notable discovery emerging from this study was the inverse relationship observed between nondimensional concentration contours and the magnitude of the chemical reaction rate. Simultaneously, it was observed that higher values of the Maxwell fluid led to a rise in the thickness of the temperature boundary layer. These findings offer valuable insights into the intricate interplay of physical and chemical phenomena in convective flows involving complex fluid properties and boundary conditions. The temperature outline diminishes as the heat generation rate increases, while the concentration profile declines with an elevation in the chemical reaction rate.
Jump-diffusion option pricing with non-IID jumps
Authors: Zou Lin , Câmara António , Li Weiping
Published: March 2024

This paper investigates how violations of the assumption that jumps are identically and independently distributed (IID) affect option prices. We characterize several types of IID jumps violations including jumps with time-varying means, time-varying variances, and time-varying autocorrelations, and analyze the combined effect of these violations on option prices. These IID violations affect option prices in different ways. Different effects of IID violations can either offset each other to eliminate the effect of isolated IID violations or can act as leverages increasing the magnitude of mispricing created by a single violation of the IID assumption. Our investigation is performed inside a new framework for the pricing of options that relaxes the assumption that jumps are IID. We derive three families of jump-diffusion option pricing formulae with non-IID jumps. Numerically and empirically, we show that the non-IID models can improve the BSM on the S&P 500 options for both in-samples and out-of-the-samples data in terms of SSE, AE and ARE.
The Security Jawbreaker
Authors: Vachon Phil
Published: March 2024

Access to a system should not imply authority to use it. Enter the principle of complete mediation.
Is There Another System?
Authors: Neville-Neil George V.
Published: March 2024

Computer science is the study of what can be automated.
Twin-Width IV: Ordered Graphs and Matrices
Authors: Bonnet Édouard , Giocanti Ugo , de Mendez Patrice Ossona , Simon Pierre , Thomassé Stéphan , Toruńczyk Szymon
Published: March 2024

We establish a list of characterizations of bounded twin-width for hereditary classes of totally ordered graphs: as classes of at most exponential growth studied in enumerative combinatorics, as monadically NIP classes studied in model theory, as classes that do not transduce the class of all graphs studied in finite model theory, and as classes for which model checking first-order logic is fixed-parameter tractable studied in algorithmic graph theory.

This has several consequences. First, it allows us to show that every hereditary class of ordered graphs either has at most exponential growth, or has at least factorial growth. This settles a question first asked by Balogh et al. [
5
] on the growth of hereditary classes of ordered graphs, generalizing the Stanley-Wilf conjecture/Marcus-Tardos theorem. Second, it gives a fixed-parameter approximation algorithm for twin-width on ordered graphs. Third, it yields a full classification of fixed-parameter tractable first-order model checking on hereditary classes of ordered binary structures. Fourth, it provides a model-theoretic characterization of classes with bounded twin-width. Finally, it settles the small conjecture [
8
] in the case of ordered graphs.
Algorithm 1044: PyGenStability, a Multiscale Community Detection Framework with Generalized Markov Stability
Authors: Arnaudon Alexis , Schindler Dominik J. , Peach Robert L. , Gosztolai Adam , Hodges Maxwell , Schaub Michael T. , Barahona Mauricio
Published: March 2024

We present PyGenStability, a general-use Python software package that provides a suite of analysis and visualization tools for unsupervised multiscale community detection in graphs. PyGenStability finds optimized partitions of a graph at different levels of resolution by maximizing the generalized Markov Stability quality function with the Louvain or Leiden algorithm. The package includes automatic detection of robust graph partitions and allows the flexibility to choose quality functions for weighted undirected, directed, and signed graphs and to include other user-defined quality functions.
Towards Hybrid-Optimization Video Coding
Authors: Huo Shuai , Liu Dong , Zhang Haotian , Li Li , Ma Siwei , Wu Feng , Gao Wen
Published: March 2024

Video coding that pursues the highest compression efficiency is the art of computing for rate-distortion optimization. The optimization has been approached in different ways, exemplified by two typical frameworks: block-based hybrid video coding and end-to-end learned video coding. The block-based hybrid framework encompasses more and more coding modes that are available at the decoder side; an encoder tries to search for the optimal coding mode for each block to be coded. This is an online, discrete, search-based optimization strategy. The end-to-end learned framework embraces more and more sophisticated neural networks; the network parameters are learned from a collection of videos, typically using gradient descent-based methods. This is an offline, continuous, numerical optimization strategy. Having analyzed these two strategies, both conceptually and with concrete schemes, this paper suggests investigating
hybrid
-optimization video coding, that is to combine online and offline, discrete and continuous, search-based and numerical optimization. For instance, we propose a hybrid-optimization video coding scheme, where the decoder consists of trained neural networks and supports several coding modes, and the encoder adopts both numerical and search-based algorithms for the online optimization. Our scheme achieves promising compression efficiency on par with H.265/HM for the random-access configuration.
Generating Python Type Annotations from Type Inference: How Far Are We?
Authors: Guo Yimeng , Chen Zhifei , Chen Lin , Xu Wenjie , Li Yanhui , Zhou Yuming , Xu Baowen
Published: March 2024

In recent years, dynamic languages such as Python have become popular due to their flexibility and productivity. The lack of static typing makes programs face the challenges of fixing type errors, early bug detection, and code understanding. To alleviate these issues, PEP 484 introduced optional type annotations for Python in 2014, but unfortunately, a large number of programs are still not annotated by developers. Annotation generation tools can utilize type inference techniques. However, several important aspects of type annotation generation are overlooked by existing works, such as in-depth effectiveness analysis, potential improvement exploration, and practicality evaluation. And it is unclear how far we have been and how far we can go.

In this paper, we set out to comprehensively investigate the effectiveness of type inference tools for generating type annotations, applying three categories of state-of-the-art tools on a carefully-cleaned dataset. First, we use a comprehensive set of metrics and categories, finding that existing tools have different effectiveness and cannot achieve both high accuracy and high coverage. Then, we summarize six patterns to present the limitations in type annotation generation. Next, we implement a simple but effective tool to demonstrate that existing tools can be improved in practice. Finally, we conduct a controlled experiment showing that existing tools can reduce the time spent annotating types and determine more precise types, but cannot reduce subjective difficulty. Our findings point out the limitations and improvement directions in type annotation generation, which can inspire future work.
Medical Question Summarization with Entity-driven Contrastive Learning
Authors: Lu Wenpeng , Wei Sibo , Peng Xueping , Wang Yi-Fei , Naseem Usman , Wang Shoujin
Published: March 2024

By summarizing longer consumer health questions into shorter and essential ones, medical question-answering systems can more accurately understand consumer intentions and retrieve suitable answers. However, medical question summarization is very challenging due to obvious distinctions in health trouble descriptions from patients and doctors. Although deep learning has been applied to successfully address the medical question summarization (MQS) task, two challenges remain: how to correctly capture question focus to model its semantic intention, and how to obtain reliable datasets to fairly evaluate performance. To address these challenges, this article proposes a novel medical question summarization framework based on
e
ntity-driven
c
ontrastive
l
earning (ECL). ECL employs medical entities present in frequently asked questions (FAQs) as focuses and devises an effective mechanism to generate hard negative samples. This approach compels models to focus on essential information and consequently generate more accurate question summaries. Furthermore, we have discovered that some MQS datasets, such as the iCliniq dataset with a 33% duplicate rate, have significant data leakage issues. To ensure an impartial evaluation of the related methods, this article carefully examines leaked samples to reorganize more reasonable datasets. Extensive experiments demonstrate that our ECL method outperforms the existing methods and achieves new state-of-the-art performance, i.e., 52.85, 43.16, 41.31, 43.52 in terms of ROUGE-1 metric on MeQSum, CHQ-Summ, iCliniq, HealthCareMagic dataset, respectively. The code and datasets are available at
https://github.com/yrbobo/MQS-ECL
Evolution from Bardeen–Cooper–Schrieffer to Bose–Einstein Condensation in Two Dimensions: Crossovers and Topological Quantum Phase Transitions
Authors: Sá de Melo C.A.R. , Van Loon Senne
Published: March 2024

We review aspects of the evolution from Bardeen–Cooper–Schrieffer (BCS) to Bose–Einstein condensation (BEC) in two dimensions, which have now become relevant in systems with low densities, such as gated superconductors Li xZrNCl, magic-angle twisted trilayer graphene, FeSe, FeSe1− xS x, and ultracold Fermi superfluids. We emphasize the important role played by chemical potentials in determining crossovers or topological quantum phase transitions during the BCS–BEC evolution in one-band and two-band superfluids and superconductors. We highlight that crossovers from BCS to BEC occur for pairing in nonnodal s-wave channels, whereas topological quantum phase transitions, in which the order parameter symmetry does not change, arise for pairing in any nodal higher angular momentum channels, such as d-wave. We conclude by discussing a few open questions regarding the BCS-to-BEC evolution in 2D, including modulus fluctuations of the order parameter, tighter upper bounds on critical temperatures, and the exploration of lattice effects in two-band superconductors and superfluids.
Prevalence of Lameness in Dairy Cows and Associated Risk Factors at Hawassa Town Dairy Farms, Ethiopia
Authors: Gessese Abebe Tesfaye , Ayele Abayineh , Kinde Mebrie Zemene , Asmare Asefa
Published: March 2024

Lameness is one of the greatest constraints on the productivity, health, and welfare of dairy cattle. A cross‐sectional study was carried out from March 2021 to September 2021 in Hawassa town with the aim of assessing the prevalence and identifying the associated risk factors of lameness in dairy farms. The study was conducted on 440 animals belonging to 19 randomly selected intensive dairy farms. Data regarding lameness and its possible risk factors were collected both at animal and farm level using a questionnaire. The results showed that the overall prevalence of lameness was 10.2% (n = 45/440). The association of lameness prevalence with various risk factors including milking status, exercise, age, parity, milk yield, and lactation stage was statistically tested using logistic regression model. There was a significant variation in the prevalence of lameness (P < 0.05) between cattle with different milking status, age, parity, milk yield, and stage of lactation by the univariable analysis result. According to the multivariable analysis, only milk yield and lactation stage were statistically associated with the occurrence of lameness. Milking animals (8%) had higher prevalence of lameness than nonmilking (2.2%). The occurrence of lameness increased with milk yield. The highest prevalence of lameness was recorded in the early stage of lactation. Lameness was more frequent in hind limbs (6.6%) than in forelimbs (3.6%). The main causes of lameness observed in this study were both claw overgrowth 10 (2.3%), unequal claw size 10 (2.3%), solar ulcer 8 (1.8%), interdigital necrobacillosis 2 (0.5%), interdigital hyperplasia 2 (0.5%), and digital dermatitis 1 (0.2%). There was no means of early lameness diagnosis in 94.7% of farms. Lameness was found to be an important disease in dairy cows at Hawassa town. Prevention and early diagnosis leading to prompt treatment of lameness in cows should be part of dairy farm management practice.
ACA-28, an ERK MAPK Signaling Modulator, Exerts Anticancer Activity through ROS Induction in Melanoma and Pancreatic Cancer Cells
Authors: Takasaki Teruaki , Hamabe Yasuyuki , Touchi Kenta , Khandakar Golam Iftakhar , Ueda Takeshi , Okada Hitoshi , Sakai Kazuko , Nishio Kazuto , Tanabe Genzoh , Sugiura Reiko
Published: March 2024

The extracellular signal-regulated kinase (ERK) MAPK pathway is dysregulated in various human cancers and is considered an attractive therapeutic target for cancer. Therefore, several inhibitors of this pathway are being developed, and some are already used in the clinic. We have previously identified an anticancer compound, ACA-28, with a unique property to preferentially induce ERK-dependent apoptosis in melanoma cells. To comprehensively understand the biological cellular impact induced by ACA-28, we performed a global gene expression analysis of human melanoma SK-MEL-28 cells exposed to ACA-28 using a DNA microarray. The transcriptome analysis identified nuclear factor erythroid 2-related factor 2 (Nrf2), a master transcription factor that combats oxidative stress, as the most upregulated genetic pathway after ACA-28 treatment. Consistently, ACA-28 showed properties to increase the levels of reactive oxygen species (ROS) as well as Nrf2 protein, which is normally repressed by proteasomal degradation and activated in response to oxidative stresses. Furthermore, the ROS scavenger N-acetyl cysteine significantly attenuated the anticancer activity of ACA-28. Thus, ACA-28 activates Nrf2 signaling and exerts anticancer activity partly via its ROS-stimulating property. Interestingly, human A549 cancer cells with constitutively high levels of Nrf2 protein showed resistance to ACA-28, as compared with SK-MEL-28. Transient overexpression of Nrf2 also increased the resistance of cells to ACA-28, while knockdown of Nrf2 exerted the opposite effect. Thus, upregulation of Nrf2 signaling protects cancer cells from ACA-28-mediated cell death. Notably, the Nrf2 inhibitor ML385 substantially enhanced the cell death-inducing property of ACA-28 in pancreatic cancer cells, T3M4 and PANC-1. Our data suggest that Nrf2 plays a key role in determining cancer cell susceptibility to ACA-28 and provides a novel strategy for cancer therapy to combine the Nrf2 inhibitor and ACA-28.
Supplementary Table 1-2 from Antibody–Drug Conjugate αEGFR-E-P125A Reduces Triple-negative Breast Cancer Vasculogenic Mimicry, Motility, and Metastasis through Inhibition of EGFR, Integrin, and FAK/STAT3 Signaling
Authors: Sankar Ankita P. , Cho Hyun-Mi , Shin Seung-Uon , Sneh Tal , Ramakrishnan Sundaram , Elledge Christian , Zhang Yu , Das Rathin , Gil-Henn Hava , Rosenblatt Joseph D.
Published: March 2024

Extended table of differentially expressed genes from 2D to 3D
FIGURE 2 from Rejuvenated iPSC-derived GD2-directed CART Cells Harbor Robust Cytotoxicity Against Small Cell Lung Cancer
Authors: Kinoshita Shintaro , Ishii Midori , Ando Jun , Kimura Takaharu , Yamaguchi Tomoyuki , Harada Sakiko , Takahashi Fumiyuki , Nakashima Kazutaka , Nakazawa Yozo , Yamazaki Satoshi , Ohshima Koichi , Takahashi Kazuhisa , Nakauchi Hiromitsu , Ando Miki
Published: March 2024

Generation of GD2-CARrejTs. A, Schema, generation of GD2-CARrejTs. T-iPSCs established from LMP2-specific CTL clones were transduced with lentiviral GD2-CAR and GD2-CAR-iPSCs were differentiated into GD2-CARrejTs. B, Flow cytometric analysis of GD2-2840z-CARTs and GD2-CARrejTs to evaluate CAR transgene expression and LMP2 antigen specificity. Histogram in blue, fluorescence minus one (FMO) control. Histogram in red, GD2-2840z-CARTs and GD2-CARrejTs. The plots represent three independent experiments. C, Intracellular perforin and granzyme B marking, GD2-2840z-CARTs and GD2-CARrejTs (red). Histogram in blue, FMO control. The plots represent three independent experiments. D, CBA for measuring cytokines (IFNγ, TNF, and IL2) produced by effector T cells (GD2-2840z-CARTs and GD2-CARrejTs) after 24 hours of coculture with SCLC-J1. Error bars represent ± SEM. E, Representative flow cytometrogram of memory phenotype (CD45RA and CD62 L population) among GD2-2840-CARTs and GD2-CARrejTs. F,In vitro51Cr assays of GD2-2840z-CARTs, GD2-CARrejTs, and control T cells against SCLC cell lines. Error bars represent ± SD. Data represent three independent triplicate experiments. G, RTCA continuous graphical output of tumor proliferation indices up to 40 hours for H69 cells cocultured with control T cells, GD2-2840z-CARTs, and GD2-CARrejTs and for tumor only; E:T ratio uniformly 1:1. Data were plotted and are shown as mean ±SD. Data represent three independent triplicate experiments. H, RTCA continuous graphical output of tumor proliferation indices up to 100 hours for H446 cells cocultured with control T cells, GD2-2840z-CARTs, and GD2-CARrejTs and for tumor only; E:T ratio uniformly 1:1. Data were plotted and are shown as mean ±SD. Data represent three independent triplicate experiments.
FIGURE 1 from Rejuvenated iPSC-derived GD2-directed CART Cells Harbor Robust Cytotoxicity Against Small Cell Lung Cancer
Authors: Kinoshita Shintaro , Ishii Midori , Ando Jun , Kimura Takaharu , Yamaguchi Tomoyuki , Harada Sakiko , Takahashi Fumiyuki , Nakashima Kazutaka , Nakazawa Yozo , Yamazaki Satoshi , Ohshima Koichi , Takahashi Kazuhisa , Nakauchi Hiromitsu , Ando Miki
Published: March 2024

Generation of GD2-CARTs. A, GD2 expression by NSCLC cell line (negative control) and by four SCLC cell lines (red), with isotype control (blue). The plots represent three independent experiments. B, Schema, lentiviral GD2-CAR-vectors containing Ubc promoter. CAR contains an scFv derived from heavy (VH) and light chain (VL) variable regions of 14G2a mAb. TM, transmembrane. Each CAR has a costimulatory domain (highlighted in red): GD2-2840z, CD28 and OX40; GD2-28z, CD28; and GD2-BBz, 4-1BB. The constructs contain the cleavable 2A-like sequence and mCherry. C, Flow cytometric analysis, GD2-CAR transgene expression in GD2-2840z-CARTs, GD2-28z-CARTs, and GD2-BBz-CARTs (red). Fluorescence minus one (FMO) control (blue). The histogram represents three independent experiments. D, Flow cytometric analysis, expression of LAG-3, PD-1, and TIM-3 on day 12 after transduction. Error bars represent ± SD. Data represent triplicate experiments. *, P < 0.05; **, P < 0.01; ***, P < 0.001, respectively by one-way ANOVA. E,In vitro51Cr release assay of GD2-2840z-CARTs, GD2-28z-CARTs, and GD2-BBz-CARTs (effectors) against GD2+ tumor cells (NK-YS). Error bars represent ± SD. Data represent triplicate experiments. F,In vitro51Cr release assay of GD2-2840z-CARTs against GD2+ SCLC. Error bars represent ± SD. Data represent three independent triplicate experiments. G, Flow cytometric analysis, MFI of GD2 on GD2-expressing tumors. Error bars represent ± SD. The bars represent triplicate experiments. H,In vitro51Cr release assay of GD2-2840z-CARTs against SCLC cell lines. Error bars represent ± SD. Data represent triplicate experiments.
Supplementary Figure 6 from Antibody–Drug Conjugate αEGFR-E-P125A Reduces Triple-negative Breast Cancer Vasculogenic Mimicry, Motility, and Metastasis through Inhibition of EGFR, Integrin, and FAK/STAT3 Signaling
Authors: Sankar Ankita P. , Cho Hyun-Mi , Shin Seung-Uon , Sneh Tal , Ramakrishnan Sundaram , Elledge Christian , Zhang Yu , Das Rathin , Gil-Henn Hava , Rosenblatt Joseph D.
Published: March 2024

Effects of α5β1 integrin and its downstream signaling components on VM tube formation
Supplementary Figure 4 from Antibody–Drug Conjugate αEGFR-E-P125A Reduces Triple-negative Breast Cancer Vasculogenic Mimicry, Motility, and Metastasis through Inhibition of EGFR, Integrin, and FAK/STAT3 Signaling
Authors: Sankar Ankita P. , Cho Hyun-Mi , Shin Seung-Uon , Sneh Tal , Ramakrishnan Sundaram , Elledge Christian , Zhang Yu , Das Rathin , Gil-Henn Hava , Rosenblatt Joseph D.
Published: March 2024

αEGFR-E-P125A treatment timecourse
Supplementary Figure 1B from Antibody–Drug Conjugate αEGFR-E-P125A Reduces Triple-negative Breast Cancer Vasculogenic Mimicry, Motility, and Metastasis through Inhibition of EGFR, Integrin, and FAK/STAT3 Signaling
Authors: Sankar Ankita P. , Cho Hyun-Mi , Shin Seung-Uon , Sneh Tal , Ramakrishnan Sundaram , Elledge Christian , Zhang Yu , Das Rathin , Gil-Henn Hava , Rosenblatt Joseph D.
Published: March 2024

Extended heatmap of differentially expressed genes