bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deciphering the low-frequency seismic signals in the Weiyuan Shale gas field: implications for reservoir and structural heterogeneity
Authors: Abbas Aqeel , Yang Hongfeng , Zi Jinping 
Published: January 2024

SUMMARY
Hydraulic fracturing (HF) often stimulates the local earthquake productivity which provides a unique opportunity to characterize the crustal heterogeneities, reservoir properties and fluid injection effects. However, the velocity models acquired solely based on the arrival time records are often undermined due to the seismic network coverage and interpolation techniques. Instead, we adopt the waveform-based approach to apprehend; (1) structural heterogeneities, (2) reservoir distribution and (3) signatures of the injected fluid in the Weiyuan shale gas field. We categorize the waveforms into dominant high and low frequencies based on the qualitative inspection and frequency index analysis of the seismic waveforms. We first inspect the waveform to access the potential controlling mechanisms (source, site and path effects) at both single and multiple stations in different azimuthal orientations. As a result, we find the path effect as a dominant factor to influence the waveform characteristics, for example S-wave amplitude, and frequency. Subsequently, to localize the path effect, we conduct an in-depth examination of events within 10 km of each seismic station and classify the waveform records using their frequency indices. Notably, certain stations record a significant proportion of low-frequency waveforms (LFWs, up to 20 per cent), while others have limited occurrences (∼1 per cent) indicating suspected anomalous zones. Afterward, we identify two suspected anomalous zones based on LFWs intensity and ray tracing map. Both zones are in close proximity to fault zones and preserved reservoirs with no HF activities, where fault damage zones or the fluid-rich reservoir may contribute to our observed LFWs.
Pindel-TD: A Tandem Duplication Detector Based on A Pattern Growth Approach
Authors: Yang Xiaofei , Zheng Gaoyang , Jia Peng , Wang Songbo , Ye Kai 
Published: January 2024

Abstract
Tandem duplication (TD) is a major type of structural variations (SVs) that plays an important role in novel gene formation and human diseases. However, TDs are often missed or incorrectly classified as insertions by most modern SV detection methods due to the lack of specialized operation on TD-related mutational signals. Herein, we developed a TD detection module for the Pindel tool, referred to as Pindel-TD, based on a TD-specific pattern growth approach. Pindel-TD is capable of detecting TDs with a wide size range at single nucleotide resolution. Using simulated and real read data from HG002, we demonstrated that Pindel-TD outperforms other leading methods in terms of precision, recall, F1-score, and robustness. Furthermore, by applying Pindel-TD to data generated from the K562 cancer cell line, we identified a TD located at the seventh exon of SAGE1, providing an explanation for its high expression. Pindel-TD is available for non-commercial use at https://github.com/xjtu-omics/pindel.
Making development assistance work for Africa: from aid-dependent disease control to the new public health order
Authors: Nonvignon Justice , Soucat Agnès , Ofori-Adu Paulina , Adeyi Olusoji 
Published: January 2024

Abstract
The Coronavirus disease (COVID-19) pandemic has revealed the fragility of pre-crisis African health systems, in which too little was invested over the past decades. Yet, development assistance for health (DAH) more than doubled between 2000 and 2020, raising questions about the role and effectiveness of DAH in triggering and sustaining health systems investments. This paper analyses the inter-regional variations and trends of DAH in Africa in relation to some key indicators of health system financing and service delivery performance, examining (1) the trends of DAH in the five regional economic communities of Africa since 2000; (2) the relationship between DAH spending and health system performance indicators and (3) the quantitative and qualitative dimensions of aid substitution for domestic financing, policy-making and accountability. Africa is diverse and the health financing picture has evolved differently in its subregions. DAH represents 10% of total spending in Africa in 2020, but DAH benefitted Southern Africa significantly more than other regions over the past two decades. Results in terms of progress towards universal health coverage (UHC) are slightly associated with DAH. Overall, DAH may also have substituted for public domestic funding and undermined the formation of sustainable UHC financing models. As the COVID-19 crisis hit, DAH did not increase at the country level. We conclude that the current architecture of official development assistance (ODA) is no longer fit for purpose. It requires urgent transformation to place countries at the centre of its use. Domestic financing of public health institutions should be at the core of African social contracts. We call for a deliberate reassessment of ODA modalities, repurposing DAH on what it could sustainably finance. Finally, we call for a new transparent framework to monitor DAH that captures its contribution to building institutions and systems.
Factors impacting sustained coverage in the context of donor transitions: experience from Sri Lanka
Authors: Perera Prasadini N , Amarasinghe Sarasi N , Fonseka Sachini H , Abeysinghe Nihal , Rannan-Eliya Ravindra P 
Published: January 2024

Abstract
Although not reliant on donor funding for health, the external assistance that Sri Lanka receives contributes to the improvement of the health system and health outcomes. In this study, we evaluated transition experiences of the expanded programme on immunization (EPI) that received Gavi funding to expand the vaccine portfolio and the Anti-Malaria Campaign (AMC) that received funding from the Global Fund for AIDS, Tuberculosis and Malaria to scale-up interventions to target and achieve malaria elimination. We assessed if EPI and AMC programmes were able to sustain coverage of previously donor-funded interventions post-transition and explain the facilitators and barriers that contribute to this. We used a mixed methods approach using quantitative data to assess coverage indicators and the financing mix of the health programmes and qualitative analysis guided by a framework informed by the Walt and Gilson policy triangle that brought together document review and in-depth interviews to identify facilitators and barriers to transition success. The EPI programme showed sustained coverage of Gavi-funded vaccines post-transition and the funding gap was bridged by mobilizing domestic financing facilitated by the Gavi co-financing mechanism, full integration within existing service delivery structures, well-established and favourable pharmaceutical procurement processes for the public sector and stewardship and financial advocacy by technically competent managers. Although the absence of indigenous cases of malaria since 2012 suggests overall programme success, the AMC showed mixed transition success in relation to its different programme components. Donor-supported programme components requiring mobilization of operational expenses, facilitated by early financial planning, were successfully transitioned (e.g. entomological and parasitological surveillance) given COVID-19-related constraints. Other key programme components, such as research, training, education and awareness that are dependent on non-operational expenses are lagging behind. Additionally, concerns of AMC’s future financial sustainability within the current structure remain in the context of low malaria burden.
Adjustments in purchasing arrangements to support the COVID-19 health sector response: evidence from eight middle-income countries
Authors: Parmar Divya , Mathauer Inke , Bloom Danielle , Dkhimi Fahdi , Abuosi Aaron Asibi , Chen Dorothee , Chukwuma Adanna , de Claro Vergil , Comsa Radu , Domingo Albert Francis , Doroshenko Olena , Gong Estelle , Goroshko Alona , Nketiah-Amponsah Edward , Lylozian Hratchia , Nkangu Miriam , Onwujekwe Obinna , Obikeze Obioma , Pattnaik Anooj , Rivillas Juan Carlos , Tapkigen Janet , Vîlcu Ileana , Wang Huihui , Wee Co Pura Angela 
Published: January 2024

Abstract
The COVID-19 pandemic has triggered several changes in countries’ health purchasing arrangements to accompany the adjustments in service delivery in order to meet the urgent and additional demands for COVID-19-related services. However, evidence on how these adjustments have played out in low- and middle-income countries is scarce. This paper provides a synthesis of a multi-country study of the adjustments in purchasing arrangements for the COVID-19 health sector response in eight middle-income countries (Armenia, Cameroon, Ghana, Kenya, Nigeria, Philippines, Romania and Ukraine). We use secondary data assembled by country teams, as well as applied thematic analysis to examine the adjustments made to funding arrangements, benefits packages, provider payments, contracting, information management systems and governance arrangements as well as related implementation challenges. Our findings show that all countries in the study adjusted their health purchasing arrangements to varying degrees. While the majority of countries expanded their benefit packages and several adjusted payment methods to provide selected COVID-19 services, only half could provide these services free of charge. Many countries also streamlined their processes for contracting and accrediting health providers, thereby reducing administrative hurdles. In conclusion, it was important for the countries to adjust their health purchasing arrangements so that they could adequately respond to the COVID-19 pandemic, but in some countries financing challenges resulted in issues with equity and access. However, it is uncertain whether these adjustments can and will be sustained over time, even where they have potential to contribute to making purchasing more strategic to improve efficiency, quality and equitable access in the long run.
The Ileal Pouch-Anal Anastomosis: Identifying Structural Disorders
Authors: Schwartzberg David M , Kayal Maia , Barnes Edward L 
Published: January 2024

Lay Summary
Chronic disorders of a pelvic pouch may result from structural complications secondary to postoperative surgical complications which manifest as a variety of symptoms. Knowing the crucial pitfalls of pouch construction can guide treatment options in patients suffering from signs of pouch failure.
Evaluating the ChatGPT family of models for biomedical reasoning and classification
Authors: Chen Shan , Li Yingya , Lu Sheng , Van Hoang , Aerts Hugo J W L , Savova Guergana K , Bitterman Danielle S 
Published: January 2024

Abstract

Objective
Large language models (LLMs) have shown impressive ability in biomedical question-answering, but have not been adequately investigated for more specific biomedical applications. This study investigates ChatGPT family of models (GPT-3.5, GPT-4) in biomedical tasks beyond question-answering.

Materials and Methods
We evaluated model performance with 11 122 samples for two fundamental tasks in the biomedical domain—classification (n = 8676) and reasoning (n = 2446). The first task involves classifying health advice in scientific literature, while the second task is detecting causal relations in biomedical literature. We used 20% of the dataset for prompt development, including zero- and few-shot settings with and without chain-of-thought (CoT). We then evaluated the best prompts from each setting on the remaining dataset, comparing them to models using simple features (BoW with logistic regression) and fine-tuned BioBERT models.

Results
Fine-tuning BioBERT produced the best classification (F1: 0.800-0.902) and reasoning (F1: 0.851) results. Among LLM approaches, few-shot CoT achieved the best classification (F1: 0.671-0.770) and reasoning (F1: 0.682) results, comparable to the BoW model (F1: 0.602-0.753 and 0.675 for classification and reasoning, respectively). It took 78 h to obtain the best LLM results, compared to 0.078 and 0.008 h for the top-performing BioBERT and BoW models, respectively.

Discussion
The simple BoW model performed similarly to the most complex LLM prompting. Prompt engineering required significant investment.

Conclusion
Despite the excitement around viral ChatGPT, fine-tuning for two fundamental biomedical natural language processing tasks remained the best strategy.
Prevalence of white spot syndrome virus (WSSV) in wild-caught and commodity decapod crustaceans in coastal South Carolina, USA
Authors: Sasson Daniel A , Allen Jacqueline M , Walker Matt J , Huber Jeanette H , Rothman Gregory K , Kingsley-Smith Peter R , Darden Tanya L , Kendrick Michael R 
Published: January 2024

Abstract
White spot syndrome virus (WSSV) is a highly contagious and economically costly virus that affects many crustacean species. Since its introduction into the United States in the 1990s, it has spread from aquaculture shrimp and crayfish to wild crustaceans throughout the southeastern United States. Transmission to natural systems may occur through contact between commodity (i.e., store-bought) and wild crustaceans or the use of infected frozen shrimp as bait, which has been proven capable of transmitting the virus. In this study, we surveyed both live (Penaeus setiferus (Linnaeus, 1767) and P. aztecusIves, 1891) and frozen commodity shrimp (Penaeus vannameiBoone, 1931) and crayfish (Procambarus troglodytes (Le Conte, 1856) and P. clarkii (Girard, 1852)) as well as wild populations of some of these species of shrimp, crayfish, and blue crabs (Callinectes sapidusRathbun, 1896) in South Carolina for WSSV. We found extremely low levels of the virus in wild-caught decapods but high levels of WSSV in commodity crayfish (50%) and imported frozen shrimp (43.3%). While additional work is needed to understand the environmental conditions that affect the transmission potential of WSSV, these results suggest that care must be taken with commodity crustaceans to prevent introductions of WSSV and subsequent harm to natural ecosystems.
Hessian fly (Diptera: Cecidomyiidae) virulence in Louisiana: assessment of field populations from 2023 to efficacy of 27 Hessian fly resistance genes in wheat
Authors: Schemerhorn Brandon J , Cambron Sue E , Subramanyam Subhashree 
Published: January 2024

Abstract
The Hessian fly, Mayetiola destructor (Say), is one of the most important insect pest plaguing wheat (Triticum aestivum, L) producers across the United States and around the world. Genetic resistance is the stalwart for control of Hessian fly. However, new genotypes (biotypes) arise in deployment of wheat containing resistance genes, so field populations must be evaluated periodically to provide information on the efficacy of those deployed genes. Louisiana (LA), with its diverse agricultural landscape, is not exempt from the challenges posed by this destructive pest. We previously documented the resistance response of wheat lines harboring Hessian fly resistance (H) genes against field populations collected in 2008 from across the southeastern United States, including Iberville Parish, LA. In the spring of 2023, we reevaluated the resistance response of 27 H genes from the field populations collected from Iberville Parish, LA, and compared the results with those observed in 2008. Sixteen H genes showed comparable resistance to the field populations from both years. While 3 of the H genes, H11, H23, and H24, showed a significant decrease in resistance, 2 genes, H16 and H31, had marked increase in resistance. Furthermore, 6 additional H genes were evaluated in 2023, with 4 showing &gt;70% resistance. Our results clearly identify a total of 20 H genes that are moderate to highly effective against the 2023 Hessian fly population from Iberville Parish, LA. The resistance response documented in this study offers valuable information to wheat breeders in the region for effective management of this insect pest.
Herbivore-induced plant volatiles emitted by citrus in response to spider mite infestation can attract predatory mites
Authors: Song Cancan , Chen Die , Jiang Chunxian , Li Chengcheng , Chen Lin , Huang Rong , Wang Xian , Qin Jie , Li Qing 
Published: January 2024

Abstract
Understanding the nutritional interplay among plants, pests, and natural enemies is essential for sustainable pest management. Enhancing the efficiency of natural enemies, such as Neoseiulus californicus (McGregor) (Acari: Phytoseiidae) is critical, and exploiting herbivore-induced plant volatiles (HIPVs) offers a promising approach. However, N. californicus has rarely been reported to utilize HIPVs to improve their biological control capabilities. Our research revealed a significant difference in the diversity of volatile compounds detected in clean Citrus reticulata Blanco leaves compared to those in C. reticulata leaves infested with Panonychus citri (McGregor) (Acari: Tetranychidae), regardless of mite presence. This suggests that P. citri infestation induces a wide array of HIPVs in C. reticulata leaves. We conducted olfactory behavioral assays to evaluate the response of N. californicus to synthetic HIPVs. Results revealed that linalool (1.00 mg/mL), 2,2,4-trimethylpentane (10.0 mg/mL), undecylcyclohexane (1.00 mg/mL), and (+)-dibenzoyl-L-tartaric anhydride (10.0 mg/mL) significantly attracted N. californicus while pentadecanal (1.00 mg/mL) significantly deterred it. A 3-component blend of linalool, undecylcyclohexane, and (+)-dibenzoyl-L-tartaric anhydride was better than other combinations in attracting N. californicus. This combination provided the basis for developing an attractant for N. californicus, facilitating the rate of its dispersal to enhance its biological control of pests. Consequently, this research offers vital insights into improving the sustainable pest control potential of predatory mites.
Crustal structure of the southern Lower Yangtze region and its geological implications: a deep reflection seismic profile
Authors: Zhang Penghui , Wang Tong , Li Guangcai , Liu Jianxun , Fang Hui , Li Pei , Li Hongkui 
Published: January 2024

Abstract
The southern part of the Lower Yangtze Region, located in the area bounded by the Jiangnan and Dabie orogenic belts, is characterized by a complex fault structure and unique magmatism, and is one of the key areas in regional tectonic evolution and magmatism. In this study the authors used a 45-km-long deep reflection seismic profile to study the crustal structure of the southern Lower Yangtze Region. The results show that the crust in the study area is ∼31.5–33.6 km thick, with the Huaining Basin as the thinnest part. A detachment surface at a depth of around 12 km divides the crust into the upper and lower crust, act as a key tectonic decoupling layer. Two sets of thrust nappe faults with opposite tendencies have horizontally developed above the detachment surface, with the Huaining Basin as the centre. A typical wedge-shaped structure has developed below the Qianshan Basin, suggesting that two sets of thrust nappe faults may have formed in the same dynamic system. The reflection patterns of the lower crust on both sides of the profile exhibit a monoclinic feature with opposite tendencies, while the lower part of the Huaining Basin exhibits an arcuate upward-arch feature. A prominent ductile shear zone in the lower crust has developed on the west side of the Huaining Basin, which can provide a favourable channel for magma migration. The results of this study deepen our understanding of the deep structure of the Lower Yangtze Region, and provide important constraint data for research on dynamic mechanisms.
Secretory expression of amylosucrase in Bacillus licheniformis through twin-arginine translocation pathway
Authors: Wang Caizhe , Niu Dandan , Mchunu Nokuthula Peace , Zhang Meng , Singh Suren , Wang Zhengxiang 
Published: January 2024

Abstract

Amylosucrase (EC 2.4.1.4) is a versatile enzyme with significant potential in biotechnology and food production. To facilitate its efficient preparation, a novel expression strategy was implemented in Bacillus licheniformis for the secretory expression of Neisseria polysaccharea amylosucrase (NpAS). The host strain B. licheniformis CBBD302 underwent genetic modification through the deletion of sacB, a gene responsible for encoding levansucrase that synthesizes extracellular levan from sucrose, resulting in a levan-deficient strain, B. licheniformis CBBD302B. Neisseria polysaccharea amylosucrase was successfully expressed in B. licheniformis CBBD302B using the highly efficient Sec-type signal peptide SamyL, but its extracellular translocation was unsuccessful. Consequently, the expression of NpAS via the twin-arginine translocation (TAT) pathway was investigated using the signal peptide SglmU. The study revealed that NpAS could be effectively translocated extracellularly through the TAT pathway, with the signal peptide SglmU facilitating the process. Remarkably, 62.81% of the total expressed activity was detected in the medium. This study marks the first successful secretory expression of NpAS in Bacillus species host cells, establishing a foundation for its future efficient production.

One-Sentence Summary
Amylosucrase was secreted in Bacillus licheniformis via the twin-arginine translocation pathway.
Two decades of endemic dengue in Bangladesh (2000–2022): trends, seasonality, and impact of temperature and rainfall patterns on transmission dynamics
Authors: Hasan Mohammad Nayeem , Khalil Ibrahim , Chowdhury Muhammad Abdul Baker , Rahman Mahbubur , Asaduzzaman Md , Billah Masum , Banu Laila Arjuman , Alam Mahbub-Ul , Ahsan Atik , Traore Tieble , Uddin Md Jamal , Galizi Roberto , Russo Ilaria , Zumla Alimuddin , Haider Najmul 
Published: January 2024

Abstract
The objectives of this study were to compare dengue virus (DENV) cases, deaths, case-fatality ratio [CFR], and meteorological parameters between the first and the recent decades of this century (2000–2010 vs. 2011–2022) and to describe the trends, seasonality, and impact of change of temperature and rainfall patterns on transmission dynamics of dengue in Bangladesh. For the period 2000–2022, dengue cases and death data from Bangladesh’s Ministry of Health and Family Welfare’s website, and meteorological data from the Bangladesh Meteorological Department were analyzed. A Poisson regression model was performed to identify the impact of meteorological parameters on the monthly dengue cases. A forecast of dengue cases was performed using an autoregressive integrated moving average model. Over the past 23 yr, a total of 244,246 dengue cases were reported including 849 deaths (CFR = 0.35%). The mean annual number of dengue cases increased 8 times during the second decade, with 2,216 cases during 2000–2010 vs. 18,321 cases during 2011–2022. The mean annual number of deaths doubled (21 vs. 46), but the overall CFR has decreased by one-third (0.69% vs. 0.23%). Concurrently, the annual mean temperature increased by 0.49 °C, and rainfall decreased by 314 mm with altered precipitation seasonality. Monthly mean temperature (Incidence risk ratio [IRR]: 1.26), first-lagged rainfall (IRR: 1.08), and second-lagged rainfall (IRR: 1.17) were significantly associated with monthly dengue cases. The increased local temperature and changes in rainfall seasonality might have contributed to the increased dengue cases in Bangladesh.