bluuebunny/crossref_metadata_2025 huggingface dataset:
Experimental research of time for opening and closing of spray in flat and injector nozzles
Authors: Onyshchenko B V , Onyshchenko V B , Nazarenko V A
Published: December 2024

Experimental studies have been carried out to determine time for opening and closing of spray in Lechler ST 110-02 and IDK 120-02 nozzels for the combined spraying working body (CWB). The spray nozzles have been filmed by digital video camera. We received the results of opening time for nozzles and calculated the arithmetic mean, average square deviation (standard), and coefficient of variation by average square deviation. The opening time(arithmetic mean) for Lechler ST 110-02 flat nozzle 0,235 s. The opening time for Lechler IDK 120-02 injection sprays nozzle 0,435 s. The average value of the closing for spray in Lechler ST 110-02 is 0.04 s, and the Lechler IDK 120-02 nozzle is 0.08 s. The transient time for switching from the ST 110-02 nozzle to the IDK 120-02 nozzle should be 0.395 s, and the switching from the IDK 120-02 nozzle to the ST 110-02 nozzle should be 0.155 s.
Management of economic security of food industry enterprises as a direction of ensuring sustainable development
Authors: Ostapchuk T P , Ye Orlova K , Denysiuk O H , Yu Biriuchenko S
Published: December 2024

The article is devoted to the peculiarities of the economic security management of food industry enterprises as a direction of ensuring sustainable development of economic entities. It was determined that the food industry plays an important role in Ukraine’s social and economic system; at the same time, food industry enterprises activity is characterized by the presence of negative trends. The essence and the components of the enterprise economic security were considered. The economic security is defined as a mechanism aimed at confronting threats and overcoming negative trends. The conceptual model of ensuring economic security of enterprises was proposed. In order to determine the key directions for increasing the level of economic security the model of dependence of economic security coefficient was formed using correlation and regression analysis. According to the model, the main factors of influence on food industry enterprises economic security formation are the growth rate of net profit, cash ratio and profitability of economic activity. The key measures for the formation of a constructive influence on the specified factors are proposed in order to increase the level of economic security of food industry enterprises.
Modeling of the energy security of the country in the context of sustainable development: the case of Ukraine
Authors: Tkalenko S I , Liubachivska R Z , Makedon H M
Published: December 2024

Ukraine’s energy industry experienced organizational and territorial challenges, resulting in a coal scarcity and a need for stable and balanced development. Ukraine’s unified energy system, which includes a variety of power plants, plays an important role in supplying electricity to other nations. The authors recommend using the multidimensionality principle and a systemic approach to examine the country’s energy security, as well as the development of a model based on energy product manufacturing under Ukraine’s tough economic and political conditions. Such a theory will show the peculiarities of the production of energy products, which is characterized by a vast collection of qualities and factors that influence it. The factors (or variables) studied in the article are classified as endogenous and exogenous. The E-Views application was used to model the country’s energy security in terms of energy product production. The outcomes of the modeling revealed the presence of long-term endogenous and exogenous factors influencing the total volume of energy product production; the existence of a strong relationship between the volume of energy product production and imports, total energy supply, and total final consumption; and opportunities for significant growth in domestic energy product production in the future. The model’s practical significance has been demonstrated through reduced reliance on imports, diversification of energy sources, energy independence, energy availability, collaboration in the field of energy security, economic growth, and environmental and sustainable development. The article concentrates the authors’ attention on Ukraine’s energy sector, which is critical to the country’s economy and supply to the EU.
Experimental tests of the over-columned plates of the precast building frame
Authors: Pavlikov A M , Harkava O V
Published: December 2024

The construction of a precast flat plate frame of buildings is considered for its implementation during the restoration of the housing stock of Ukraine. The analysis of the precast flat plate floor system of the frame structural system by using the yield line method showed that in the ultimate state the floor is divided into separate discs along the joints of precast plates. This makes it possible to determine the load-bearing capacity of the floor by considering each plate taking into account their supporting and loading conditions. Based on this, experimental tests of three full-size over-columned plates of a precast flat plate floor system are carried out, according to the diagram closest to the actual scheme of their operation as part of the floor. The general deflections of the plates, moments of crack formation and width of their opening, as well as strains of concrete and reinforcement in characteristic cross-sections of the plates are determined. Based on the experimental tests, the accepted failure scheme of the over-columned plates of the precast flat plate floor system is confirmed and the feasibility of applying the yield line method to the calculation of their bearing capacity is proven.
Propagation of elastic waves in cross-sectionally heterogeneous rods
Authors: Zdeshchyts A V , Zdeshchyts V M
Published: December 2024

The article is devoted to measuring the propagation speed of elastic waves in metal rods of variable cross-section. The paper examines the dependence of the speed measure of propagation of elastic waves on the geometric and physical characteristics of the rods. The research methods are based on the use of known statements of the impact theory during the collision of a ball with the end of a metal rod. Solid rods, stepped rods, and rods with axisymmetric holes of different depths were experimentally studied. A piezo sensor connected to a digital oscilloscope was used to record pressure fluctuations at the end of the rod. The method of least squares was used for processing and further analysis of experimental data. Theoretical and experimental studies proved that there are two characteristic areas in which the speed of propagation of an elastic wave in a non-homogeneous cross-sectional rod differs from the value of the wave speed in a one-dimensional rod. A sinusoidal functional dependence of the propagation speed of the elastic wave on the caliber of the rod was obtained.
Comparison of the seismic loading of points on the surface of the Earth during a massive explosion in a mine
Authors: Zdeshchyts A V , Zdeshchyts V M
Published: December 2024

Geomechanical studies are performed at almost all large mining enterprises in the world. As a result of industrial activity, the Kryvyi Rih region has developed serious environmental problems. The mining of ore in Kryvyi Rih region led to the formation of numerous underground cavities. Hundreds of square kilometers of the Earth’s surface were in zones of mass collapse. Therefore, diagnosis and control of the stress state of the massif of rocks are relevant. Along with the processes of movement of underground cavities to the Earth’s surface, there is a constant threat of destruction or damage to residential buildings, violation of the integrity of the massif due to mass explosions in quarries and mines. These explosions also affect the rate at which voids emerge. This leads not only to unpredictable exits of funnels and the development of landslides, but also to the threat of rock strikes in mines. The article considers the method of measuring the vector velocity of soil particle oscillations from one source in different directions at the same time. The purpose of this article is to compare the seismic load of points on the Earth’s surface during an explosion in a mine with their orthogonal location along the directions under the conditions of destruction of the rock body in a separate area. The main task of the research was to determine the intensity of seismic explosion vibrations near the foundations of residential buildings and industrial buildings in the area of the industrial site of the mine, which were located in opposite directions. The main result of the work is obtaining a set of data related to the amplitude and frequency characteristics of seismic waves that have passed through a half-kilometer layer of rock.
Improvement in the evaluation of gamma radiation from cylindrical bodies with spatially inhomogeneous source activity distribution
Authors: Popov O O , Skurativskyi S I , Molitor N , Koniushkov A , Fomichova O V , Svitlyshyn I I
Published: December 2024

Radioactivity and radioactive materials are constant companions of our life. Therefore, their studies and utilization are an important part of the development of human society. One of lines of work with radioactivity of various media concerns their gamma ray spectrometry which covers the issues of mineral exploration, ecological monitoring, medicine, security, agriculture, anti-terrorist protection, assessment of the consequences of man-made and natural disasters, etc. The tasks of spectroscopy include the description, survey, and analysis of gamma fields produced by natural environment or artificial objects. To solve these tasks effectively, mathematical modeling based on the fundamental physical laws of radioactivity and modern achievements of mathematics and informatics is used. In particular, in this research, we consider the gamma radiation from the cylindrical body and develop the procedure for assessing the gamma flux intensity when the source activity is inhomogeneously distributed over the body volume. The procedure is a semi-analytic approach and is based on the representation of the source activity function as a linear combination of step functions. Physically it means the approximation of inhomogeneous body by a layered medium. The procedure also allows one to get an analytical expression for the gamma flux intensity which is observed at the axes of symmetry of the cylindrical body. It is performed the comparison of approximate and exact values of intensity for exponential source activity function when analytical integration is possible. We also discuss the procedure application to the case when the source activity function is nonmonotonic and restrictions of procedure use appear.
Investigation of changes in the intensity of polished surface glow of natural stone depending on the intensity of its heating
Authors: Korobiichuk V V , Kryvoruchko A O , Bilobrov D M
Published: December 2024

In this publication, the authors consider the influence of high temperatures on the change in the intensity of the gloss of the front surface of products made of acidic and basic rocks of natural stone. Changes in gloss intensity were analyzed for each of the control points of heating for the front surface of samples of acidic and basic rocks of natural stone. The main factors affecting the change in the intensity of the gloss of the front surface of products made of acidic and basic natural stone are determined. It has been established that when heated (exposure to high temperatures), acidic rocks of natural stone lose their luster less intensively than rocks with a basic composition. The greatest loss of luster upon heating (exposure to high temperatures) is characteristic of labradorite. On the basis of the obtained values, it is possible to predict the change in the intensity of the gloss of the front polished surface of products from basic and acidic natural stone after exposure to high temperatures, as well as to control the quality of the front surface of natural stone products to obtain products with specified parameters for restoration or restoration work.
The influence of the war on the content of some components in the rivers of Ukraine
Authors: Litynska M I , Pelekhata O B
Published: December 2024

As a result of hostilities, the surface waters of Ukraine may be polluted by various components. This can significantly affect the safety of drinking water supply and the ability of water bodies to self-clean. The article is devoted to the calculation of modified water pollution indices and the assessment of water pollution for some Ukrainian rivers that may have been affected by the war. We calculated the modified water pollution index and assessed water pollution for 7 points of 5 Ukrainian rivers (Desna, Dnipro, Styr, Siversky Donets and Oskil) that may have been affected by the war. The modified water pollution index also included nitrates and polyphosphates, unlike the conventional water pollution index. River conditions were assessed from 2018 to 2023 in order to compare water quality in these rivers before and after active hostilities began in February 2022. The most significant effect of military operations on water quality in 2022 was seen at the Siversky Donets and Oskil rivers in the Kharkiv and Donetsk regions, where there were numerous ongoing hostilities. Pollution by biogenic components did not exceed the self-cleaning capacity of these rivers, but bioremediation methods can be used to accelerate the return to normal conditions. Despite being in a conflict zone in the spring of 2022, this had minimal impact on the water quality of the Desna and Dnipro rivers near Kyiv in the summer of 2022. The water quality of the Styr river was improved due to absence of active military actions near the river and significant decrease in tourism and agricultural use of territories.
Assessment of the distribution and population characteristics of Musculium lacustre Müller, 1774 (Mollusca, Bivalvia, Sphaeriidae) in anthropogenically altered aquatic landscapes of the northern right bank of the Dnipro River in Ukraine
Authors: Shevchuk L M , Bylyna L V , Vasilieva L A , Herasymchuk O L , Vakaliuk T A
Published: December 2024

Today, the rapid disappearance of bivalves in European water bodies is a matter of serious concern. The state of study of mollusks of the family Sphaeriidae in Europe, including Ukraine, is considered insufficient, which does not allow to assess their resources, develop measures for protection and restoration of their numbers. The paper assesses the distribution and frequency of occurrence of the small bivalve Musculium lacustre Müller, 1774 (Mollusca, Bivalvia, Sphaeriidae) in the anthropogenically altered aquatic landscapes of the northern right bank of the Dnipro River of Ukraine. This species is considered to be quite eutopian, but in the surveyed region it shows a clear tendency to decrease the frequency of occurrence and population density of individuals. The reason for this situation is the disappearance of typical habitats due to the transformation of rivers into a system of ponds and reservoirs as a result of dam construction and pollution. Out of 232 sites analyzed, M. lacustre was found in the Pripyat sub-basin in only 5 sites, and in the Teteriv basin (Middle Dnipro sub-basin) in only 2 sites (the frequency of occurrence in these sub-basins is 4% each, and the overall figure for the sampling area is 3%. The maximum population density was 21 in the Hnylopyat River, 11 in the Gusak River, and 1-3 ind./m2 in other sampling sites, although according to literature data, in the last century it could reach several thousand per m2 in Ukraine. Found in rivers and streams, it prefers flowing areas.
Regulation of water flow on the foothills on the Ukrainian Carpathians rivers with the use of flooded groynes
Authors: Shynkaruk L A , Volk L R , Dovbenko I E
Published: December 2024

Based on the results of extensive laboratory studies of regulatory and protective structures – groynes, carried out in the hydrotechnical laboratory of National University of Water and Environmental Engineering (NUWEE), recommendations for the design, construction, and operation of structures have been developed. The method of hydraulic calculation of groynes is presented. According to these recommendations, a system of structures with experimental types of groynes on the foothills of the rivers of the Ukrainian Carpathians was designed and built. Surveys were carried out on objects of various types of groynes after the passage of floods on the rivers of the specified region. The causes of deformations of buildings and their destruction have been established. The influence of the existing groynes on the channel process has been studied. Conclusions were drawn on the further use of groynes structures as regulatory and protective structures in the foothills of rivers.
Concession as a tool for improving the budget and tax incentives for investment attractiveness of the tourist complex in Ukraine
Authors: Krushinska A V , Samaricheva T A , Arziantseva D A , Zakharkevych N P , Hrytsenko O M
Published: December 2024

The argumentation of the use of concession of historical and architectural objects in Ukraine as a tool for improving the budget and tax incentives for investment attractiveness of the tourist complex has been carried out. A scientific approach to budgetary and tax incentives for investment attractiveness of tourist facilities has been formed using an optimization model for calculating concession payments, which ensures the flexibility of incentives, takes into account the interests of investors, based on indicators for assessing the effectiveness of an investment project with a simultaneous focus on maximizing budget revenues. It is substantiated that the budgetary and tax incentives for investment attractiveness of tourist complexes through the introduction of public-private partnership in the form of a concession of historical and architectural objects will allow private business to invest in attractive tourist sites and ensure higher profitability of the hotel and restaurant business, since the interests of the investor are taken into account, and will also reduce budget expenditures and increase tax revenues to the budgets from servicing tourist flows.
The impact of low-molecular carboxylic acids on carbon dioxide corrosion of steel in underground gas production equipment in the Dnipro-Donetsk basin fields
Authors: Dmytrenko V I , Zezekalo I G , Peremetchyk A V , Matsui A M
Published: December 2024

The work carried out a set of experimental studies to reduce the activity of corrosion processes in underground well equipment. Corrosion of downhole equipment is a complex heterogeneous process. In the complex of factors influencing both magnitude and intensity of corrosion damage, low molecular weight water-soluble carboxylic acids play a significant role. The features of metal-carbon dioxide corrosion (CO2 corrosion) in production well fluid have been established depending on low molecular weight carboxylic acids. It has been revealed that the influence of carboxylic acids in field wells in the initial period of development is reduced to the destruction of protective carbonate films formed as a result of carbon dioxide corrosion of the metal surface. The highest corrosion rate is at the beginning of droplet water condensation since the main factors influencing the corrosion rate (acid concentration and temperature) are greatest at this point. It has been established that the interaction of organic acids with metal occurs in the Dnipro-Donetsk basin fields at the temperature range of 90-110°C and a depth of 3000-3500 m. The interval of action of organic acids on the metal of tubing pipes depends on the regime constancy and operating time of the well. In constant mode, the effect of organic acids is limited to 100-150 m. The effect of corrosion under the influence of organic acids is especially pronounced in wells where the carbon dioxide content is insignificant. The influence of corrosion products on the process speed has been determined. Iron salts of carboxylic acids, formed as a result of corrosion during condensation of aqueous fluid in a well, are subsequently inhibitors of carbon dioxide corrosion of gas industry equipment.
The current state and development prospects of the graphite industry of Ukraine
Authors: Lozhnikov O V , Pavlychenko A V , Shustov O O , Dereviahina N I
Published: December 2024

The article is devoted to establishing the current state of graphite deposits development in Ukraine and the prospects of supplying industry with this critical raw material. The countries with the largest production of natural graphite and Ukraine’s share of the world market have been determined. Global trends in graphite consumption in industry and its impact on market value have been established. The mining and geological conditions of typical graphite deposits occurrence have been determined, which indicates the expediency of surface mining. The geological characteristics of the largest graphite deposits of Ukraine have been studied, which allows further research to determine directions for increasing the efficiency of beneficiation of graphite raw materials and to increase the greening of production. The main areas of graphite use in high-tech sectors of the economy are given, which confirms the critical role of this raw material in the creation of renewable energy chains. Estimated reserves of graphite have been established in the most significant graphite deposits of Ukraine, which include Zavallivske, Petrivske, Troitske, Mariupolske, Balakhivske and Burtynske. The estimated content of graphite in the ore of the main deposits has been determined, which makes it possible to forecast the country’s resource availability with this critical raw material in the future.
Ecological Risk Assessment of Heavy Metals in the Soil at reclaimed solid waste landfill
Authors: Serafimova Ekaterina
Published: December 2024

Environmental pollution with heavy metals is a problem for most developing or emerging countries. The study investigated the concentrations of arsenic (As), nickel (Ni), chromium (Cr), nickel (Ni), zinc (Zn), cobalt (Co), copper (Cu), and lead (Pb) in 10 samples of reclaimed soil for environmental risk assessment and spatial distribution following The Municipal Solid Waste Depot in Central Northern Bulgaria. According to Bulgarian legislation, the measured average concentrations of arsenic are below the maximum permissible concentration. Using the obtained heavy metal data, pollution indices such as geoaccumulation index (Igeo), pollution factor (CF), ecological risk factor (Er), pollution degree (Cdeg), and pollution index (PLI) were calculated and the results obtained categorized the site as uncontaminated. This suggests that the studied area is well-reclaimed and does not pose an ecological risk. The findings presented in this work support data on heavy metal contamination and risk assessment in Bulgaria. This research may have benefits for trace heavy metal pollution prevention and future monitoring studies of the region.
Effect of HIV and Malaria in Pregnancy on Pertussis-specific Antibodies and Transplacental Antibody Transfer: A Secondary Analysis of a Prospective Cohort Study in Mozambican Pregnant Women and Their Infants
Authors: Bardají Azucena , Dobaño Carlota , Alonso Selena , Vala Anifa , Pantoja P. Efrain , Vidal Marta , Maculuve Sonia , Nhacolo Arsenio , Rupérez María , Morató Alba , Quintó Llorenç , Sevene Esperança , Macete Eusebio , Mayor Alfredo , Menéndez Clara , Moncunill Gemma , González Raquel
Published: December 2024

Background:

Infection during pregnancy may affect maternal and infant immunity against childhood diseases. We aimed to evaluate the effects of maternal HIV and malaria on maternal and infant pertussis immunity and placental antibody transfer.

Methods:

A prospective study was conducted in mother-infant pairs in Mozambique. Peripheral and cord blood samples were collected for pertussis-specific immune assays. Maternal HIV serostatus and Plasmodium falciparum infection were assessed. The placental transfer was assessed using cord-to-mother ratios of IgG against pertussis toxin (PT), pertactin (PRN) and fimbriae 2/3 (FIM).

Results:

A total of 270 mother-infant pairs were included: 99 mothers with HIV and 40 mothers with malaria. Pregnant women with HIV showed a reduction in placental transfer [PT: 12.7%, 95% confidence interval (CI): 2.6–21.7, P = 0.015; PRN: 14.6%, 95% CI: 6.3–22.1, P = 0.001; and FIM: 7.5%, 95% CI: −6.6 to 19.7, P = 0.282] compared with women without HIV. A trend toward reduction in IgG transfer was observed among women with malaria (PT: 9.5%, 95% CI: −4.2 to 21.4, P = 0.165; PRN: 5.0%, 95% CI: −7.0 to 15.7, P = 0.394; and FIM: 15.9%, 95% CI: −0.9 to 30.0, P = 0.062) compared with those without. Maternal HIV infection (odds ratio: 4.43, 95% CI: 2.14–9.1; P < 0.001) and high viral load (odds ratio: 4.37, 95% CI: 1.4–12.2; P = 0.033) were associated with impaired placental transfer.

Conclusions:

Maternal HIV infection is associated with lower mother-to-infant transfer of pertussis antibodies. While efforts continue in the health care of pregnant women with HIV, interventions such as maternal immunization can be a valuable strategy to prevent pertussis in infants.
Optimizing the Evaluation of Letters of Recommendation for Obstetrics and Gynecology Residency Applicants
Authors: Morales-Ramirez Pedro , Gutierrez Erick , DeMier Brettany , White-Hammonds Preslie , Mishek Henry , Dasgupta Arhita
Published: December 2024

OBJECTIVE:

To develop and validate a ChatGPT-powered tool for assessing letters of recommendation in obstetrics and gynecology residency applicants.

METHODS:

This study was conducted in two phases at a university-based obstetrics and gynecology residency program. During the development phase, 30 letters of recommendation were used to create ChatGPT prompts based on a validated scoring rubric that assesses phrases, letter features, and applicant abilities. ChatGPT scores were compared with benchmarks using intraclass correlation coefficients (ICCs) to evaluate reliability, and ChatGPT processing times were measured against those of human reviewers. In the second phase (validation), 88 letters of recommendation from residents with and without academic deficiencies (n=30) were analyzed using the ChatGPT prompts developed and refined in the first stage. Residents with academic deficiencies (case group) were matched 1:1 with a control group of residents without noted deficiencies by medical school, gender, and training period. The letter of recommendation scores between the case and control groups then were compared using the Mann-Whitney U test.

RESULTS:

ChatGPT significantly reduced review time per letter, from 7.2 minutes to 45 seconds. Inter-rater reliability between ChatGPT and benchmark scores indicated strong agreement for specific phrases (ICC 0.82, 95% CI, 0.75–0.88), moderate agreement for letter features (ICC 0.75, 95% CI, 0.68–0.82), and fair agreement for applicant abilities (ICC 0.70, 95% CI, 0.62–0.78). After refinement, ICCs improved to 0.92 (95% CI, 0.88–0.95), 0.81 (95% CI, 0.74–0.87), and 0.77 (95% CI, 0.69–0.84). Mean letter of recommendation scores for specific phrases differed significantly between residents with deficiencies (4.49; 95% CI, 3.29–5.68) and residents in the control group (6.00; 95% CI, 5.00–7.00) (P=.017). Subgroup analysis showed an even greater gap between residents with multiple deficiencies (2.15; 95% CI, 1.42–3.38) and residents in the control group (6.00; 95% CI, 5.00–7.00; P<.001), suggesting a higher predictive value for at-risk residents.

CONCLUSION:

ChatGPT can enhance the residency selection process by providing reliable letter of recommendation analysis significantly faster than human reviewers and effectively identifying key phrases in letters of recommendation that could predict future academic deficiencies.
High-fidelity disentangled cellular embeddings for large-scale heterogeneous spatial omics via DECIPHER
Authors: Xia Chen-Rui , Cao Zhi-Jie , Gao Ge
Published: December 2024

The functional role of a cell, shaped by the sophisticated interplay between its molecular identity and spatial context, is often obscured in current spatial modeling. Aiming to model large-scale heterogeneous spatial data in silico properly, DECIPHER produces high-fidelity disentangled embeddings, not only achieving superior performance in systematic benchmarks, but also empowering various real-world applications. We further demonstrated that DECIPHER is scalable to atlas-scale datasets, enabling global analysis which is largely infeasible to current state-of-the-arts.
Enhanced methods for genetic assays inDrosophilacells
Authors: Wang Y , Lee JY , Housden AE , Hottinger E , Housden BE
Published: December 2024

Genetic assays are an invaluable tool for both fundamental biological research and translational applications. Variable Dose Analysis (VDA) is an RNAi-based method for cell-based genetic assays that offers several advantages over approaches such as CRISPR and other RNAi-based methods including improved data quality (signal-to-noise ratio) and the ability to study essential genes at sub-lethal knockdown efficiency. Here we report the development of three new variants of the VDA method called high-throughput VDA (htVDA), VDA-plus and pooled-VDA. htVDA requires 10-fold reduced reagent volumes and takes advantage of liquid handling automation to allow higher throughput screens to be performed while maintaining high data quality. VDA-plus is a modified version of VDA that further improves data quality by 4.5-fold compared to standard VDA to allow highly sensitive detection of weak phenotypes. Finally, Pooled VDA allows greatly increased throughput by analysing multiple gene knockdowns in a single population of cells. Together, these new methods enhance the toolbox available for genetic assays, which will prove valuable in both high-and low-throughput applications. In particular, the low noise and ability of VDA to study essential genes at sub-lethal knockdown levels will support identification of novel drug-targets, among which essential genes are often enriched. While these tools have been developed inDrosophilacells, the underlying principles are transferrable to any cell culture system.
High-dimensional spectral flow cytometry of activation and phagocytosis by peripheral human polymorphonuclear leukocytes
Authors: Lamb Evan R. , Glomski Ian J. , Harper Taylor A. , Solga Michael D. , Criss Alison K.
Published: December 2024

Polymorphonuclear lymphocytes (PMNs) are terminally differentiated phagocytes with pivotal roles in infection, inflammation, tissue injury, and resolution. PMNs can display a breadth of responses to diverse endogenous and exogenous stimuli, making understanding of these innate immune responders vital yet challenging to achieve. Here, we report a 22-color spectral flow cytometry panel to profile primary human PMNs on population and single cell levels for surface marker expression of activation, degranulation, phagocytosis, migration, chemotaxis, and interaction with fluorescently labeled cargo. We demonstrate the surface protein response of PMNs to phorbol ester stimulation compared to untreated controls in an adherent PMN model with additional analysis of intra- and inter-subject variability. PMNs challenged with the Gram-negative bacterial pathogenNeisseria gonorrhoeaerevealed infectious dose-dependent changes in surface marker expression in bulk, population-level analysis. Imaging flow cytometry complemented spectral cytometry, demonstrating that fluorescence signal from labeled bacteria corresponded with bacterial burden on a per-cell basis. Spectral flow cytometry subsequently identified surface markers which varied with direct PMN-bacterium association as well as those which varied in the presence of bacteria but without phagocytosis. This spectral panel protocol highlights best practices for efficient customization and is compatible with downstream approaches such as spectral cell sorting and single-cell RNA-sequencing for applicability to diverse research questions in the field of PMN biology.

Summary Sentence

Here we report a 22-color spectral flow cytometry panel to profile primary human PMNs for markers of activation, degranulation, phagocytosis, migration, and chemotaxis using phorbol ester stimulation and bacterial challenge as proofs-of-concept.
Ex-vivo expansion of patient-derived PBMCs preferentially results in effector memory T-cell proliferation with restored autologous efficiency in HBV-HCC
Authors: Kah Janine , Staffeldt Lisa , Mattert Gregor , Volz Tassilo , Voß Maximilian , Schulze Kornelius , Heumann Asmus , Dandri Maura , Lüth Stefan
Published: December 2024

Background

T-cell-based therapies achieved milestones in targeting solid tumors, such as hepatocellular carcinoma, by leveraging the cytotoxic potential of effector memory T-cells. However, a key challenge lies in the ex-vivo expansion of functional memory T-cells while simultaneously preventing over-differentiation into senescent TEMRA cells.

Methods

PBMC derived from 10 HCC patients and two healthy donors were used for expansion in small bioreactors equipped with a permeable membrane for 2 weeks. During expansion, surface marker composition, cytokine and chemokine production were observed. Enriched T-cell subsets from three patients with chronic HBV infection were analysed in detail. We extracted the enriched complement of one chronically infected patient to elucidate the therapeutic potential.

Results

We successfully expanded the effector T-cell subsets for all investigated samples and consistently enriched the cell amount over time. Subsequently, we showed that the expanded patient-derived T-cells showed functionality against autologous liver cancer-derived cells by inducing receptor and protein-mediated cell death.

Conclusion

We showed the consistent ex-vivo expansion of T-cell subsets of initial patient-derived PBMCs. The enriched subsets exhibit cytotoxic functionality and shift to cytolytic TEMRA cells in an immune evasion setting in the context of chronic HBV-infected patient-derived liver cancer cells.
abCAN: a Practical and Novel Attention Network for Predicting Mutant Antibody Affinity
Authors: Gong Chen , Shen Yunyao , Liu Hongde , Ming Wenlong
Published: December 2024

Accurate prediction of mutation effects on antibody-antigen interactions is critical for antibody engineering and drug design. In this study, we present abCAN, a practical and novel attention network designed to predict changes in binding affinity caused by mutations. abCAN requires only the pre-mutant antibody-antigen complex structure and mutation information to perform its predictions. abCAN introduces an innovative approach, Progressive Encoding, which progressively integrates structural, residue-level, and sequential information to construct the complex representation in a systematic manner, effectively capturing both the topological features of the structure and contextual features of the sequence. During which, extra weight to interface residues would also be applied through attention mechanisms. These learned representations are then transferred to a predictor that estimates changes in antibody-antigen binding affinity induced by mutations. On the benchmark dataset, abCAN achieved a root-mean-square error (RMSE) of 1.195 (kcal/mol-1) and a Pearson correlation coefficient (PCC) of 0.841, setting a new state-of-the-art (SOTA) benchmark for prediction accuracy in the field of antibody affinity prediction.
Implantable 3D printed multiplexed microtunnels for spinal cord injury treatment
Authors: Grebenyuk Sergei , Medvediev Volodymyr , Rybachuk Oksana , Sheremet Yevhenii , Abdallah Ibrahim , Ustymenko Valeriia , Pivneva Tetyana , Ranga Adrian , Belan Pavel , Voitenko Nana
Published: December 2024

3D printed scaffolds offer a promising strategy for treating spinal cord injury (SCI). Here we present an innovative biotechnological approach for free-form 3D printing of scaffolds with a biomimetic architecture at a spatial resolution of up to a micrometer, designed for implantation in treatment of SCI in Wistar rats. The fabrication of scaffolds was based on 2-photon photopolymerization of organic polymers and was scalable to lesion geometries. The scaffolds were implemented as multiple densely packed squared parallel microtunnels (50 μm per side) running their entire length. These microtunnels are separated by thin walls (5–10 μm), rendering the scaffolds nearly hollow while maximizing their internal surface area. This design provides an optimal substrate, spatially aligned in the rostro-caudal direction, to support axonal and vascular ingrowth. We have found that the scaffolds, implanted in the excision of the lateral half-fragment of the spinal cord at the low thoracic level demonstrated excellent integration with surrounding tissue without the formation of a significant gliofibrous scar. Myelinated axons and oligodendrocytes, as well as vessels were observed in each microtunnel of the implanted scaffolds in 12 weeks after the operation with at least 1000 axons regenerating in the scaffold throughout its whole length. The treatment significantly improved motor function and reduced spasticity in the ipsilateral paretic limb by 8th week, with recovery sustained for at least 20 weeks. Thus, 3D oriented hollow scaffolds having a large internal surface area and direct continues microtunnels, effectively reducing axonal dispersion, mimic natural structure of the recipient tissue and create conditions for enhancing spinal cord regeneration and recovery of the motor function of the paretic limb.
Predicting antimicrobial class specificity of small molecules using machine learning
Authors: Gadiya Yojana , Genilloud Olga , Bilitewski Ursula , Brönstrup Mark , von Berlin Leonie , Attwood Marie , Gribbon Philip , Zaliani Andrea
Published: December 2024

Whilst the useful armory of antibiotic drugs is continually depleted due to the emergence of drug-resistant pathogens, the development of novel therapeutics has also slowed down. In the era of advanced computational methods, approaches like machine learning (ML) could be one potential solution to help reduce the high costs and complexity of antibiotic drug discovery and attract collaboration across organizations. In our work, we developed a large antimicrobial knowledge graph (AntiMicrobial-KG) as a repository for collecting and visualizing publicin-vitroantibacterial assay. Utilizing this data, we build ML models to efficiently scan compound libraries to identify compounds with the potential to exhibit antimicrobial activity. Our strategy involved training seven classic ML models across six compound fingerprint representations, of which the Random Forest trained on the MHFP6 fingerprint outperformed, demonstrating an accuracy of 75.9% and Cohen’s Kappa score of 0.68. Finally, we illustrated the model’s applicability for predicting the antimicrobial properties of two small molecule screening libraries. Firstly, the EU-OpenScreen library was tested against a panel of Gram-positive, Gram-negative, and Fungal pathogens. Here, we unveiled that the model was able to correctly predict more than 30% of active compounds for Gram-positive, Gram-negative, and Fungal pathogens. Secondly, with the Enamine library, a commercially available HTS compound collection with claimed antibacterial properties, we predicted its antimicrobial activity and pathogen class specificity. These results may provide a means for accelerating research in AMR drug discovery efforts by carefully filtering out compounds from commercial libraries with lower chances of being active.
Systematic analysis of immune cell motility leveraging Immunemap, an open intravital microscopy atlas
Authors: Pizzagalli Diego Ulisse , Carrillo-Barbera Pau , Palladino Elisa , Ceni Kevin , Thelen Benedikt , Pulfer Alain , Moscatello Enrico , Cabini Raffaella Fiamma , Textor Johannes , Wortel Inge M. N. ,   The Immunemap project consortium, Krause Rolf , Gonzalez Santiago Fernandez
Published: December 2024

Studying the spatiotemporal dynamics of cells in living organisms is a current frontier in bioimaging. Intravital Microscopy (IVM) provides direct, long-term observation of cell behavior in living animals, from tissue to sub-cellular resolution. Hence, IVM has become crucial for studying complex biological processes in motion and across scales, such as the immune response to pathogens and cancer. However, IVM data are typically kept in private repositories inaccessible to the scientific community, hampering large-scale analysis that aggregates data from multiple laboratories.

To solve this issue, we introduce Immunemap, an atlas of immune cell motility based on an Open Data platform that provides access to over 58’000 single-cell tracks and 1’049’000 cell-centroid annotations from 360 videos in murine models.

Leveraging Immunemap and unsupervised learning, we systematically analyzed cell trajectories, identifying four main patterns of cell migration in immune cells. Two patterns correspond to behaviors previously characterized: directed movement and arresting. However, we identified two other patterns, characterized by low directionality and twisted paths, often considered random migration. We show that the newly defined patterns can be subdivided into two distinct types: within small areas, suggesting a focused patrolling around one or a few cells, and over larger areas, indicative of a more extended tissue patrolling. Furthermore, we show that the percentage of cells displaying these motility patterns changes in response to immune stimuli.

Altogether, Immunemap embraces the FAIR principles, promoting data reuse to extract novel insights from immune cell dynamics through an image-based systems biology approach.
Cas9-based enrichment for targeted long-read metabarcoding
Authors: Nikolaeva-Reynolds Lucia , Cammies Christopher , Crichton Rosemary , Gorochowski Thomas E.
Published: December 2024

Metabarcoding is a valuable tool for characterising the communities that underpin the functioning of ecosystems. However, current methods often rely on PCR amplification for enrichment of marker genes. PCR can introduce significant biases that affect quantification and is typically restricted to one target loci at a time, limiting the diversity that can be captured in a single reaction. Here, we address these issues by using Cas9 to enrich marker genes for long-read nanopore sequencing directly from a DNA sample, removing the need for PCR. We show that this approach can effectively isolate a 4.5 kb region covering partial 18S and 28S rRNA genes and the ITS region in a mixed nematode community, and further adapt our approach for characterising a diverse microbial community. We demonstrate the ability for Cas9-based enrichment to support multiplexed targeting of several different DNA regions simultaneously, enabling optimal marker gene selection for different clades of interest within a sample. We also find a strong correlation between input DNA concentrations and output read proportions for mixed-species samples, demonstrating the ability for quantification of relative species abundance. This study lays a foundation for targeted long-read sequencing to more fully capture the diversity of organisms present in complex environments.
Thermosensory neurons control genetic inheritance through regulation of germline transposons
Authors: Szántó Péter R. , Meyer David H. , Teichman Guy , Pérez-Llanos Francy J. , Rickert Daniel , Köhrer Karl-Erich , Rechavi Oded , Schumacher Björn
Published: December 2024

Epigenetic inheritance can be influenced by environmental conditions and somatic inputs originating from different tissues. Such transgenerational inheritance is reversable as it does not lead to mutations and thus alterations in the genetic information. Epigenetic mechanisms such as small RNAs (sRNAs) in the germline silence transposable elements (TEs), which comprise a significant portion of the genome. TE mobility can be mutagenic and is thought to contribute to genome evolution by altering genome structure and diversification. InC. eleganselevated temperature leads to desilencing of TEs in the germline, suggesting that environmental conditions could impact the integrity of inheritable genomes. Here, we show that dysfunction of the AFD thermosensory neurons leads to desilencing of TEs in the germline. The TE activity results inde novoinsertions and mutagenesis. Our data indicate that neuronal sensing of environmental conditions can alter genetic inheritance through stress-induced TE mutagenesis thus shaping genome evolution.
Human iPSC-derived motor neuron innervation enhances the differentiation of muscle bundles engineered with benchtop fabrication techniques
Authors: Santoso Jeffrey W , Do Stephanie K , Verma Riya , Do Alexander V , Hendricks Eric , Ichida Justin K , McCain Megan L
Published: December 2024

Engineered skeletal muscle tissues are critical tools for disease modeling, drug screening, and regenerative medicine, but are limited by insufficient maturation. Because innervation is a critical regulator of skeletal muscle development and regeneration in vivo, motor neurons are hypothesized to improve the maturity of engineered skeletal muscle tissues. Although motor neurons have been added to pre-engineered muscle constructs, the impact of motor neurons added prior to the onset of muscle differentiation has not been evaluated. In this study, benchtop fabrication equipment was used to facilely fabricate chambers for engineering 3-dimensional (3-D) skeletal muscles bundles and measuring their contractile performance. Primary chick myoblasts were embedded in an extracellular matrix hydrogel solution and differentiated into engineered muscle bundles, with or without the addition of human induced pluripotent stem cell (hiPSC)-derived motor neurons. Muscle bundles differentiated with motor neurons had neurites distributed throughout their volume and a higher myogenic index compared to muscle bundles without motor neurons. Innervated muscle bundles also generated significantly higher twitch and tetanus forces in response to electrical field stimulation after one and two weeks of differentiation compared to non-innervated muscle bundles cultured with or without neurotrophic factors. Non-innervated muscle bundles also experienced a decline in rise and fall times as the culture progressed, whereas innervated muscle bundles and non-innervated muscle bundles with neurotrophic factors maintained more consistent rise and fall times. Innervated muscle bundles also expressed the highest levels of the genes for slow myosin light chain 3 (MYL3) and myoglobin (MB), which are associated with slow twitch fibers. These data suggest that motor neuron innervation enhances the structural and functional development of engineered skeletal muscle constructs and maintains them in a more oxidative phenotype.