bluuebunny/crossref_metadata_2025_split huggingface dataset:
Expanding America’s Biological and Chemical Warfare Programs
Authors: Parasidis Efthimios 
Published: December 2024

Abstract
This chapter details America’s post-WWII programs in chemical and biological warfare. Although international treaties limited the situations under which a nation could deploy biological or chemical weapons, the agreements did not restrict research, development, or stockpiling. Coupled with the military’s biological and chemical warfare programs, the military and CIA collaborated with dozens of universities, hospitals, and research institutes on mind control projects with hallucinogenic drugs. As with atomic and radiation studies, haphazard adherence to research subject protections was a hallmark of these programs. In many instances, studies involving service members were deemed training exercises; in others, clandestine research was conducted on unsuspecting civilians. Projects sought to enhance military preparedness and garner knowledge on offensive and defensive measures: this included weaponization of pathogens, field tests with biological weapons, development of mind-altering drugs for use in military and intelligence operations, and formulation of noxious chemicals that could devastate enemy forces, land, and food supplies.
OpenVariant: a toolkit to parse and operate multiple input file formats
Authors: Martínez-Millán David , Brando Federica , L. Grau Miguel , Sánchez-Guixé Mònica , López-Elorduy Carlos , Reyes-Salazar Iker , Deu-Pons Jordi , López-Bigas Núria , González-Pérez Abel 
Published: December 2024

Abstract

Summary
Advances in high-throughput DNA sequencing technologies and decreasing costs have fueled the identification of small genetic variants (such as single nucleotide variants and indels) across tumors. Despite efforts to standardize variant formats and vocabularies, many sources of variability persist across databases and computational tools that annotate variants, hindering their integration within cancer genomic analyses. In this context, we present OpenVariant, an easily extendable Python package that facilitates seamless reading, parsing and refinement of diverse input file formats in a customizable structure, all within a single process.

Availability and implementation
OpenVariant is an open-source package available at https://github.com/bbglab/openvariant. Documentation may be found at https://openvariant.readthedocs.io.
A near-tight lower bound on the density of forward sampling schemes
Authors: Kille Bryce , Groot Koerkamp Ragnar , McAdams Drake , Liu Alan , Treangen Todd J 
Published: December 2024

Abstract

Motivation
Sampling k-mers is a ubiquitous task in sequence analysis algorithms. Sampling schemes such as the often-used random minimizer scheme are particularly appealing as they guarantee at least one k-mer is selected out of every w consecutive k-mers. Sampling fewer k-mers often leads to an increase in efficiency of downstream methods. Thus, developing schemes that have low density, i.e. have a small proportion of sampled k-mers, is an active area of research. After over a decade of consistent efforts in both decreasing the density of practical schemes and increasing the lower bound on the best possible density, there is still a large gap between the two.

Results
We prove a near-tight lower bound on the density of forward sampling schemes, a class of schemes that generalizes minimizer schemes. For small w and k, we observe that our bound is tight when k≡1(mod w). For large w and k, the bound can be approximated by 1w+k⌈w+kw⌉. Importantly, our lower bound implies that existing schemes are much closer to achieving optimal density than previously known. For example, with the current default minimap2 HiFi settings w = 19 and k = 19, we show that the best known scheme for these parameters, the double decycling-set-based minimizer of Pellow et al. is at most 3% denser than optimal, compared to the previous gap of at most 50%. Furthermore, when k≡1(mod w) and the alphabet size σ goes to ∞, we show that mod-minimizers introduced by Groot Koerkamp and Pibiri achieve optimal density matching our lower bound.

Availability and implementation
Minimizer implementations: github.com/RagnarGrootKoerkamp/minimizers ILP and analysis: github.com/treangenlab/sampling-scheme-analysis.
Inflammation during oocyte maturation reduces developmental competence and increases apoptosis in blastocysts
Authors: Tariq Arslan , Seekford Zachary K , Bromfield John J 
Published: December 2024

Abstract
Uterine infections cause ovarian dysfunction and infertility. The bacterial endotoxin, lipopolysaccharide, accumulates in the follicular fluid of dominant follicles of cows with uterine infections. Granulosa cells produce an innate inflammatory response to lipopolysaccharide, altering the follicular microenvironment of the oocyte. We hypothesized that developmental competence and embryo quality would be reduced when oocytes are matured in an inflammatory environment. Bovine mural granulosa cells were exposed to either 1 μg/mL of lipopolysaccharide or medium alone for 24 h to produce a conditioned medium. Inflammatory responses of mural granulosa cells were confirmed by increased expression of CXCL8, IL1B, IL6, and TNF. Bovine cumulus–oocyte complexes were matured for 22 ± 1 h in a medium supplemented with either 1 μg/mL of lipopolysaccharide, 10% v/v conditioned medium of granulosa cells treated with either lipopolysaccharide (LCM) or medium alone, or no supplementation. In addition, polymyxin B (20 μg/mL) was added to the maturation medium to sequester LPS. Following maturation, cumulus–oocyte complexes were fertilized and cultured for 7.5 days with no further treatment. Oocyte maturation using lipopolysaccharide or LCM impaired development to the blastocysts stage, reduced the number of total and CDX2-negative blastomeres, and increased TUNEL-positive cells in blastocysts. Polymyxin B could rescue these effects in the lipopolysaccharide group but not in the LCM group, indicating factors produced by granulosa cells and not lipopolysaccharide alone compromised oocyte development. These findings suggest that the inflammatory milieu produced by granulosa cells in response to lipopolysaccharide impairs oocyte competence and the quality of resultant blastocyst-stage embryos.
Generating training events for building cyber-physical security skills
Authors: Vineetha Harish Avanthika , Tam Kimberly , Jones Kevin 
Published: December 2024

Abstract
As the threat of cyber attacks increases, the cyber security sector continues to train professionals as one form of mitigation. Gamification and infrastructure like cyber ranges (CRs) have been proven useful in training cyber security specialists to detect and react to cyber-attacks in information technology. However, a subset of all digital threats target cyber-physical systems (CPS), not just information systems, and these threats have been growing rapidly in recent years. While those threats are increasing, training specific to cyber-physical threats is not growing as quickly as information technology training solutions. While CRs are useful for training and supporting events like cyber defence exercises and capture the flags events, limitations to CRs make it more difficult to make an immersive event for cyber-physical training. This paper demonstrates how to devise a cyber-physical training environment using a combination of CRs and CPS testbeds,and how to devise an accompanying immersive scenario to improve cyber-physical security skills through cooperative learning. To do this, an example training was created and implemented. This paper concludes with the results of running this event four times.
Enhancing security of medical images using code-based intermittent encryption and convolutional neural network
Authors: Aruchamy Prasanth , Sundarrajan M , Choudhry Mani Deepak , Jothi Akshya 
Published: December 2024

Abstract
There has recently been a rise in the demand for telemedicine systems that securely and effectively transmit medical pictures. Cognitive radio (CR) significantly uses the unutilized spectrum by using the notion of spectrum sensing. Like certain other patient records, medical imaging data has strict requirements for security and anonymity. This makes sending healthcare picture information via an exposed system difficult because of the problems identified and the risks associated with massive data spillage. This study suggests a reliable CR technology with an image encryption technique to transmit medical images securely. In the proposed approach, the convolutional neural network method has been employed for complaisant spectrum sensing, where the Fusion Center trains the network for classification tasks using historical sensing data. Due to the proper training, the system runs in a time-slotted fashion. The proposed method provides an actor-critic transfer learning technique for a secondary user to select its processing method to raise confidence level while observing energy constraints. Finally, the numerical simulation results are examined to assess the suggested approaches under various configurations related to peak signal-to-noise ratio and structural similarity index which provide 90% more efficiency than the traditional simulated techniques.
Dual transcatheter edge-to-edge repair in a patient with cardiac amyloidosis and severe secondary mitral and tricuspid regurgitation: a case report
Authors: Vogel Julia , Luedike Peter , Mahabadi Amir Abbas , Rassaf Tienush , Michel Lars 
Published: December 2024

Abstract

Background
Mitral and tricuspid regurgitation in patients with cardiac amyloidosis (CA) pose significant diagnostic and therapeutic challenges due to its non-specific symptoms and limited treatment options. Transcatheter edge-to-edge repair (TEER) is complicated by altered cardiac geometry, advanced restriction, and potential amyloid valve deposits.

Case summary
We present the case of dual TEER in a 79-year-old male with advanced transthyretin cardiac amyloidosis (ATTR-CA) and severe symptomatic mitral and tricuspid regurgitation. In a staged approach, TEER for both the mitral and tricuspid valves was successfully conducted, resulting in improved valvular function and symptom relief. Transvalvular gradients were 5 mmHg for mitral valve and 2 mmHg for tricuspid valve, each with mild residual regurgitation, improved clinical status, and regressive natriuretic peptides.

Discussion
This case underscores the feasibility of dual TEER in CA patients with valvular involvement. Further research is necessary to optimize treatment strategies and address the multifaceted nature of this complex disease.
A perfect mimic: the role of multimodality imaging in right ventricular cardiomyopathy—a case report
Authors: Viskin Dana , Laufer-Perl Michal , Topilsky Yan , Banai Shmuel , Khoury Shafik 
Published: December 2024

Abstract

Background
Distinguishing right ventricular cardiac sarcoidosis (RVCS) from arrhythmogenic right ventricular cardiomyopathy (ARVC) is often a challenging task particularly when imaging findings are limited to the right ventricle and when electrocardiographic and arrhythmic findings are typical for ARVC. Here, we discuss the challenges of diagnosis and management in a patient whose initial work-up strongly suggested ARVC and was later diagnosed with cardiac sarcoidosis (CS), highlighting the role of multimodality imaging.

Case summary
On presentation, this patient displayed electrocardiographic abnormalities, arrhythmia morphology, and cardiac magnetic resonance imaging findings consistent with the criteria for a definite diagnosis of ARVC. However, through the use of multimodal imaging, a final diagnosis of CS was made. Subsequent immunosuppressive treatment effectively managed the inflammation, and as a primary prevention measure, an implantable cardioverter-defibrillator was implanted. Almost 2 years following the initial presentation, the patient received an appropriate shock from the device, attributed to rapid ventricular tachycardia arising from myocardial scarring.

Discussion
Right ventricular cardiac sarcoidosis can closely resemble ARVC, making it challenging to distinguish between the two. Multimodality imaging is pivotal for accurate diagnosis and risk assessment, as well as for adjusting immunosuppressive therapy and monitoring response to treatment in CS.
Beyond access to sanitary pads: a comprehensive analysis of menstrual health scheme impact among rural girls in Northeast India
Authors: Achuthan Krishnashree , Khobragade Sugandh , Kolil Vysakh Kani 
Published: December 2024

Abstract
Menstrual hygiene management (MHM) among girls in rural India poses a substantial challenge for public health, education, and quality of life, exacerbated by limited access to and affordability of menstrual products. In response to these issues, the Government of India initiated the Menstrual Hygiene Scheme (MHS) to enhance access and awareness. This study evaluates the impact of the MHS in Assam and Tripura, designated as “treatment states” with consistent pad supply from 2017 to 2021 compared to neighboring “control states” with negligible pad distribution. Utilizing data from two National Family Health Surveys, NFHS-4 and NFHS-5, and employing the propensity score matching difference-in-differences approach, we isolated the causal effect of the MHS distribution program. The key findings reveal a significant rise in sanitary pad and hygienic method usage in the treatment states, particularly among girls aged 15–19 years who received pads during the survey period. Their sanitary pad usage increased by 10.6 percentage points [95% confidence interval (CI) (0.046, 0.167)], and adoption of hygienic methods overall saw a 13.8 percentage point [95% CI (0.087, 0.188)] jump. Notably, younger girls aged 15–19 years also experienced a 6.1-percentage point [95% CI (0.004, 0.118)] increase in their understanding of ovulation, showcasing the MHS’s potential to go beyond providing products and promoting menstrual health awareness. A rise in reported sexually transmitted infections in both age groups, with a statistically significant 1.8-percentage point [95% CI (0.004, 0.032)] increase for younger girls, warrants further exploration. Disparities in impact were observed, with girls with high media exposure and greater autonomy demonstrating greater improvements in hygienic practices, highlighting the importance of information dissemination and empowering girls. Most socioeconomic groups, except the highest wealth and education levels, witnessed rises in hygienic method usage, indicating the scheme’s potential to reduce inequalities while hinting at the need for tailored interventions for marginalized communities.
Application research of artificial intelligence algorithms in energy-efficient design for low-carbon building landscapes
Authors: Zhang Jianhua , Zhan Qinchuan , Liang Haipeng 
Published: December 2024

Abstract
The study focuses on a resort hotel, exploring from multiple facets how energy-saving concepts can be integrated into landscape design to enhance customer satisfaction. By employing the analytic hierarchy process and the fuzzy comprehensive evaluation model, and optimizing the placement of architectural landscape facilities based on the Adaptive Niche Genetic Algorithm, the study strives to enhance resource efficiency while ensuring the aesthetic quality of the landscape. The research findings indicate that the hotel’s landscape design performs well overall and offers targeted optimization suggestions, thereby promoting the practical application of energy-saving landscape design principles.
Evaluation and improvement of personalized recommendation system in low-carbon network marketing
Authors: Li Dan , Yang Xin 
Published: December 2024

Abstract
As an advanced online marketing tool, the personalized recommendation system achieves precise recommendations by analyzing product and user-behavior data, thereby enhancing user experience and satisfaction. This paper proposes a recommendation algorithm based on product attributes and contexts, specifically for low-carbon online marketing. The incorporation of context weights aids the algorithm in more effectively comprehending user needs within specific contexts. Comparative experiments with collaborative filtering and content-based recommendation methods reveal that the hybrid recommendation system proposed in this paper outperforms in terms of recommendation accuracy and user satisfaction, providing theoretical support for low-carbon online marketing.
Strain phylogroup and environmental constraints shape Escherichia coli dynamics and diversity over a 20-year human gut time series
Authors: Condamine Bénédicte , Morel-Journel Thibaut , Tesson Florian , Royer Guilhem , Magnan Mélanie , Bernheim Aude , Denamur Erick , Blanquart François , Clermont Olivier 
Published: December 2024

Abstract
Escherichia coli is an increasingly antibiotic-resistant opportunistic pathogen. Few data are available on its ecological and evolutionary dynamics in its primary commensal niche, the vertebrate gut. Using Illumina and/or Nanopore technologies, we sequenced whole genomes of 210 E. coli isolates from 22 stools sampled during a 20-year period from a healthy man (ED) living in Paris, France. All phylogroups, except C, were represented, with a predominance of B2 (34.3%), followed by A and F (19% each) phylogroups. Thirty-five clones were identified based on their haplogroup and pairwise genomic single nucleotide polymorphism distance and classified in three phenotypes according to their abundance and residence time: 25 sub-dominant/transient (52 isolates), five dominant/transient (48 isolates) and five dominant/resident (110 isolates). Four over five dominant/resident clones belonged to B2 and closely related F phylogroups, whereas sub-dominant/transient clones belonged mainly to B1, A and D phylogroups. The long residence times of B2 clones seemed to be counterbalanced by lower colonization abilities. Clones with larger within-host frequency persisted for longer. By comparing ED strain genomes to a collection of commensal E. coli genomes from 359 French individuals, we identified ED-specific genomic properties including an enrichment in genes involved in a metabolic pathway (mhp cluster) and the presence of a very rare antiviral defense island. The E. coli colonization within the gut microbiota was shaped by both the intrinsic properties of the strain lineages, in particular longer residence of phylogroup B2, and the environmental constraints such as diet or phages.
Insuring the Weak: The Institutional Power Equilibrium in International Organizations
Authors: Daßler Benjamin , Heinkelmann-Wild Tim , Huysmans Martijn 
Published: December 2024

Abstract
Materially powerful states tend to dominate both the creation of international organizations (IOs) as well as subsequent IO policymaking. Materially weak states are nevertheless expected to participate in IOs since it is generally assumed that they will still profit from cooperation and prefer power to be exercised through institutions. Yet, we know surprisingly little about how exactly institutional rules protect weak states from the powerful in IOs. This paper develops a theory of institutional design that specifies the institutional power equilibrium at the heart of IOs’ constitutional treaties. Through the inclusion of veto or exit rights, weak states obtain formal safeguards against exploitation by the powerful during an IO’s operation. This expectation of a power equilibrium in IOs’ design is borne out in design patterns within the constitutional treaties of IOs created between 1945 and 2005. Our results indicate that the distribution of power among an IO’s founding members indeed affects the inclusion of institutional safeguards in their constitutional treaties and that veto and exit rights are functional substitutes in this regard. Our findings matter since the institutional power equilibrium at IO creation has important implications for relations between the materially powerful and the weak during IO operations.
Frequencies and mechanisms of mutational resistance to ceftibuten/avibactam in Enterobacterales
Authors: Mushtaq Shazad , Vickers Anna , Doumith Michel , Garello Paolo , Woodford Neil , Livermore David M 
Published: December 2024

Abstract

Background
Antibiotic resistance complicates treatment of urinary infections, particularly when these ascend above the bladder, with few oral options remaining. New oral β-lactamase inhibitor combinations present a potential answer, with ceftibuten/avibactam—now undergoing clinical trials—widely active against strains with ESBLs and serine carbapenemases. To inform its development we undertook mutant selection studies.

Methods
Single-step mutants were sought from Enterobacterales (n = 24) with AmpC, ESBL, OXA-48 and KPC β-lactamases. MICs were determined by CLSI agar dilution. Illumina WGS of selected mutants (n = 50) was performed.

Results
Even at low MIC multiples, mutant frequencies were mostly only c. 10−8. β-Lactamase structural mutants were obtained only from KPC and AmpC enzymes. The KPC mutants had Trp105Arg or Ser130Thr substitutions, causing only small MIC shifts; the AmpC mutant had an Asn346Trp replacement, as previously selected with other avibactam combinations. No ESBL mutants were obtained. Rather, from Escherichia coli, we predominantly selected mutants with modifications to ftsI, encoding penicillin-binding protein (PBP) 3. From Klebsiella pneumoniae and Enterobacter cloacae we predominantly obtained variants with modification of uptake and efflux components or their regulators. ftsI mutants lacked cross-resistance to other avibactam combinations; uptake mutants had broader MIC rises. A few putative mutants had other lesion(s) of uncertain significance, or grew as small, stressed colonies lacking detectable lesions.

Conclusions
There seems little risk of ESBLs mutating to confer ceftibuten/avibactam resistance, though some risk may apply for KPC and AmpC enzymes. The propensity to select E. coli ftsI/PBP3 mutants is notable and was not seen with other avibactam combinations.
The impact of the COVID-19 pandemic on the antimicrobial stewardship workforce in Scottish acute care hospitals—a qualitative study
Authors: Matuluko Ayodeji , Ness Valerie , Macdonald Jennifer , Sneddon Jacqueline , Seaton Ronald Andrew , Currie Kay 
Published: December 2024

Abstract

Background
Antimicrobial stewardship (AMS) programmes seek to reduce the risk of antimicrobial resistance by minimizing inappropriate antimicrobial use. The SARS-CoV-2 coronavirus (COVID-19) pandemic was characterized by initial widespread use of antimicrobials in patients with COVID-19, with potential negative effects on AMS efforts.

Objective
To explore the impact of the pandemic on the AMS workforce in Scottish acute care hospitals.

Method
Individual, semi-structured online interviews were conducted with a purposive sample of clinical staff who had an AMS focused role in Scottish Health Boards. Interviews explored staff experiences of facilitating AMS during the pandemic. Data were analysed using inductive content analysis.

Results
Thirteen staff from seven of 15 Scotland Health Boards participated. The data revealed negative (including staff redeployment and shortages) and positive effects (including improved working relationships and use of technology) on the AMS workforce. Notably, greater appreciation of the work of the AMS team was a positive outcome.

Conclusions
The robust qualitative methods applied in this original study have generated greater understanding of factors that impeded AMS services in Scotland during the pandemic. These findings may resonate internationally. Adaptation to technology and investment in the workforce are recommended to improve the resilience of AMS services in future crises.