Miracle-dz/UniFAR-FTUs huggingface dataset:
Zooming in on the intracellular microbiome composition of bacterivorous Acanthamoeba isolates

Abstract Acanthamoeba, a free-living amoeba in water and soil, is an emerging pathogen causing severe eye infection known as Acanthamoeba keratitis. In its natural environment, Acanthamoeba performs a dual function as an environmental heterotrophic predator and host for a range of microorganisms that resist digestion. Our objective was to characterize the intracellular microorganisms of phylogenetically distinct Acanthamoeba spp. isolated in Australia and India through directly sequencing 16S rRNA amplicons from the amoebae. The presence of intracellular bacteria was further confirmed by in situ hybridization and electron microscopy. Among the 51 isolates assessed, 41% harboured intracellular bacteria which were clustered into four major phyla: Pseudomonadota (previously known as Proteobacteria), Bacteroidota (previously known as Bacteroidetes), Actinomycetota (previously known as Actinobacteria), and Bacillota (previously known as Firmicutes). The linear discriminate analysis effect size analysis identified distinct microbial abundance patterns among the sample types; Pseudomonas species was abundant in Australian corneal isolates (P < 0.007), Enterobacteriales showed higher abundance in Indian corneal isolates (P < 0.017), and Bacteroidota was abundant in Australian water isolates (P < 0.019). The bacterial beta diversity of Acanthamoeba isolates from keratitis patients in India and Australia significantly differed (P < 0.05), while alpha diversity did not vary based on the country of origin or source of isolation (P > 0.05). More diverse intracellular bacteria were identified in water isolates as compared with clinical isolates. Confocal and electron microscopy confirmed the bacterial cells undergoing binary fission within the amoebal host, indicating the presence of viable bacteria. This study sheds light on the possibility of a sympatric lifestyle within Acanthamoeba, thereby emphasizing its crucial role as a bunker and carrier of potential human pathogens.
Zinc-Dependent Histone Deacetylases in Lung Endothelial Pathobiology

A monolayer of endothelial cells (ECs) lines the lumen of blood vessels and, as such, provides a semi-selective barrier between the blood and the interstitial space. Compromise of the lung EC barrier due to inflammatory or toxic events may result in pulmonary edema, which is a cardinal feature of acute lung injury (ALI) and its more severe form, acute respiratory distress syndrome (ARDS). The EC functions are controlled, at least in part, via epigenetic mechanisms mediated by histone deacetylases (HDACs). Zinc-dependent HDACs represent the largest group of HDACs and are activated by Zn2+. Members of this HDAC group are involved in epigenetic regulation primarily by modifying the structure of chromatin upon removal of acetyl groups from histones. In addition, they can deacetylate many non-histone histone proteins, including those located in extranuclear compartments. Recently, the therapeutic potential of inhibiting zinc-dependent HDACs for EC barrier preservation has gained momentum. However, the role of specific HDAC subtypes in EC barrier regulation remains largely unknown. This review aims to provide an update on the role of zinc-dependent HDACs in endothelial dysfunction and its related diseases. We will broadly focus on biological contributions, signaling pathways and transcriptional roles of HDACs in endothelial pathobiology associated mainly with lung diseases, and we will discuss the potential of their inhibitors for lung injury prevention.
The Design and Performance of the Zephyr Geodetic Antenna

The Trimble Zephyr Geodetic Antenna is a new highperformance GPS antenna utilizing two key technological innovations, for which US patents 5,515,057 and 5,694,136 have been issued to Trimble Navigation Ltd. This paper explains these GPS antenna technologies, their advantages and presents the results of performance testing on this new antenna design. The n-point antenna feed technology is described. This is designed to reduce the electrical phase center error ellipsoid through enhanced antenna element and feed point pattern symmetry. This symmetry is also designed to improve the Right Hand Circular Polarization Characteristics of the antenna, resulting in enhanced GPS signal tracking and improved multipath rejection in cases where a polarization reversal has taken place as a result of the signal reflection. The second key technology described is that utilized in the Trimble Stealth Ground Plane, an integral component of the Zephyr Geodetic Antenna. Conventional GPS ground planes typically use one of two designs; the circular metal ground plane or the choke ring ground plane. The method used for the Trimble Stealth Ground Plane is one whereby the e-field of the electromagnetic wave is cut off before it can reach the GPS antenna element. This is achieved through the use of a material in which the sheet resistivity increases exponentially along any radial line out from the antenna element to the edge of the ground plane. The use of this material offers the advantages of lighter weight and lower cost over conventional ground plane designs. As the name suggests, the material was developed out of research conducted as part of the development of the Stealth aircraft. This method is frequency independent at L-band, so is expected to be equally effective at the L1 and L2 frequencies. This property also offers a potential advantage in future triple-frequency antennas capable of tracking L1, L2 and L5 signals, with the ability to reject multipath equally effectively at all three frequencies. In order to test the performance of the new design, a number of tests were carried out with well known designs such as the choke ring used as a control. The results of these tests, including low and high elevation tracking performance, code and carrier phase multipath rejection, phase center repeatability and positioning precision are presented. Physical characteristics such as size and weight are also compared.
The possible positive effects of physical exercise on the global motion perception aging: the cognitive mechanism

Background Sensitivity to global motion perception (GMP) decreases gradually with age, and the mechanism to effectively alleviate its aging process is still unclear. This study aimed to examine the impact and mechanism of exercise on GMP aging. Methods This study adopted the global motion direction discrimination task and used motion coherence thresholds to assess GMP sensitivity. It adopted the perceptual template model (PTM) to fit the GMP processing efficiency. Results The threshold for the elderly group with no exercise was higher than that of the elderly group with exercise, while the threshold of the latter was higher than that of the youth group. The results of the model fitting showed that both models, Aa and Af, corresponding to the elderly group with exercise and the elderly group with no exercise, respectively, were the best-fitted models when compared with that of the youth group. Compared to the elderly group with no exercise, models Aa and Af, were the best-fitted models. Conclusion These results showed that good exercise habits might have a certain degree of positive effect on GMP aging, by lower their internal additive noise (Aa), and improve the ability to eliminate external noise (Af).
A Compact Fault Tolerant 2-D Anemometer

A compact anemometer capable of detecting both the magnitude and the direction of the wind in 2-D is presented. The device relies on a recently formalized principle, consisting in combining the differential pressures measured across distinct diameters of a cylinder exposed to the wind to estimate the wind velocity and the incidence angle. The cylinder includes an ad hoc microfluidic structure with three sections of diametric pressure probes connected in parallel. The multisection approach has been adopted in order to increase the reliability of the device. The prototype has been fabricated with stereolithographic printing, while commercial differential pressure sensors with low power consumption are used to read the pressures. The results of detailed experiments performed in a wind tunnel in the range 4–30 m/s are reported. A maximum angular error of 6° and a speed relative error less than 5.3% have been obtained.
Effect of Micro-Pile Mitigation on Seismic Performance of Liquefiable Ground

Soil liquefaction and its associated ground failures, pose a significant threat, causing damage to engineering structures during earthquakes, and one of the most effective methods used to mitigate liquefaction in liquefied soil is micro-pile (MP) method. Therefore, this study aims to examine the current state of MP method as liquefaction countermeasure in the soil of the Coal Fired Power Station in Central Java, an area with a high liquefaction potential. A three-dimensional finite element analysis, conducted with OpenseesPL software, uses a numerical method to yield information about ground lateral deformation and excess pore pressure generation caused by MP method during seismic shaking. This result examines important design parameters, including diameter, spacing, length of MP, and inclination of ground, to address these issues. MP method increases the stiffness of soil, reducing excessive pore pressure and thereby minimizing liquefaction risks. In general, MP remediation appeared effective for any sloping ground. This study provides valuable information for devising an efficient remediation solution by comparing relevant variables, such as diameter, spacing, MP length, and ground inclination, under the same conditions. Numerical simulation with OpenseesPL yields results such as stress and strain path, acceleration time histories, excess pore pressure, displacement time histories, and maximum lateral displacement, which are then compared with various diameter parameters. The diY6-ameter parameters were compared to test how the additional diameter dimension affects the performance of the micropile provided to the soil. This will be demonstrated based on the results shown on excess pore pressure and maximum lateral displacement. This comparison shows that increasing MP diameter is more effective in reducing the risk of liquefaction.
Attenuation of Love and Rayleigh waves across the Pacific at periods between 15 and 110 seconds

Average surface-wave attenuation coefficient values along with their 95 per cent confidence limits are determined at periods between 15 and 110 sec for paths across the Pacific Ocean. Values for the fundamental Rayleigh-mode decrease from 3.2 × 10−4km−1 at a period of 15 sec to about 0.95 × 10−4km−1 at the longest periods. Love-wave attenuation coefficient values decrease from 3.8 × 10−4km−1 to about 0.95 × 10−4km−1 over the same period range. Although these values are tentatively taken to correspond to the fundamental Love-mode, higher-mode contamination may bias the observed attenuation coefficient values over the short-period portion of the period range. Attenuation coefficient values for both Rayleigh and Love waves are higher than values previously determined for the stable interior of North America over much of the period range between 15 and 40 sec. Theoretical seismograms were computed and used as an aid in evaluating the effects of continental margin complexities and higher-mode interference on the attenuation coefficient determinations. Results indicate that the relatively large confidence limits for Rayleigh waves, especially at shorter periods, may reflect continental margin complexities. Higher-mode interference in combination with continental margin complexities produce even greater uncertainty in the determination of the attenuation coefficients for Love waves.
Utilizing Massively Parallel Sequencing (MPS) of Human Leukocyte Antigen (HLA) Gene Polymorphism to Assess Relatedness in Deficiency Parentage Testing

In the realm of DNA testing with legal implications, the reliability and precision of genetic markers play a pivotal role in confirming or negating paternity claims. This study aimed to assess the potential utility of human leukocyte antigen (HLA) gene polymorphism through massively parallel sequencing (MPS) technology as robust forensic markers for parentage testing involving genetic deficiencies. It sought to redefine the significance of HLA genes in this context. Data on autosomal short tandem repeat (aSTR) mutational events across 18 paternity cases involving 16 commonly employed microsatellite loci were presented. In instances where traditional aSTR analysis failed to establish statistical certainty, kinship determination was pursued via HLA genotyping, encompassing the amplification of 17 linked HLA loci. Within the framework of this investigation, phase-resolved genotypes for HLA genes were meticulously generated, resulting in the definition of 34 inherited HLA haplotypes. An impressive total of 274 unique HLA alleles, which were classified at either the field 3 or 4 level, were identified, including the discovery of four novel HLA alleles. Likelihood ratio (LR) values, which indicated the likelihood of the observed data under a true biological relationship versus no relationship, were subsequently calculated. The analysis of the LR values demonstrated that the HLA genes significantly enhanced kinship determination compared with the aSTR analysis. Combining LR values from aSTR markers and HLA loci yielded conclusive outcomes in duo paternity cases, showcasing the potential of HLA genes and MPS technology for deeper insights and diversity in genetic testing. Comprehensive reference databases and high-resolution HLA typing across diverse populations are essential. Reintegrating HLA alleles into forensic identification complements existing markers, creating a potent method for future forensic analysis.
Clinical utility of and correlation between Sniffin' Sticks and TIB smell identification test (TIBSIT) among Hong Kong Chinese with or without chronic rhinosinusitis

Introduction Olfactory dysfunction (OD) is common among patients with chronic rhinosinusitis (CRS). Validated and culturally specific tests, such as the “Sniffin’ Sticks” test (SST) and the TIB Smell Identification Test (TIBSIT), are crucial for the diagnosis and monitoring of OD. However, they have not been utilised in Hong Kong Chinese and their correlations are unknown. Methods Twelve CRS patients and twenty healthy volunteers were prospectively recruited from a joint allergy-otorhinolaryngology clinic in Hong Kong and performed both SST and TIBSIT. Demographics, baseline characteristics and all test results were compared and analysed. Results Patients with CRS demonstrated significantly lower test scores than healthy controls (all p < 0.001). Significant and strong correlations were observed between all composite and subtest scores, particularly between the composite SST and TIBSIT scores (ρ = 0.789, p < 0.001). Multivariate analysis demonstrated that the presence of CRS and increasing age were significantly associated with OD. Conclusion Both SST and TIBSIT are useful olfactory tests and are strongly correlated among Hong Kong Chinese. We advocate that either test can be used for measuring OD among CRS patients.
The Geography of Crime: Examining the Distribution of Break and Enters Across Regina Neighbourhoods Using Geographic Information Systems (GIS)

ii ACKNOWLEDGEMENTS . iii TABLE OF CONTENTS . v LIST OF TABLES AND FIGURES.viii CHAPTER ONE – INTRODUCTION . 1 1. The Research Context . 1 2. The Geography of Crime . 4 3. The Research Problem . 6 4. The Research Questions . 7 a. Primary Research Question.7 b. Secondary Research Questions . 7 5. Operational Definitions . 8 a. Calls for Service . 8 b. Break and Enter.8 c. Hot Spots and Hot Dots of Crime . 10 d. Geographical Crime Analysis . 10 e. Crime Mapping . 11 f. Geographic Information System (GIS) . 11 g. Other Types of Crime Analysis . 12 6. Organization of the Thesis . 12 CHAPTER TWO – REVIEW OF THE LITERATURE . 15
Using a Model and Forecasted Weather to Predict Forage and Livestock Production for Making Stocking Decisions in the Coming Growing Season

Forecasting peak standing crop (PSC) for the coming grazing season can help ranchers make appropriate stocking decisions to reduce enterprise risks. Previously developed PSC predictors were based on short-term experimental data (<15 yr) and limited stocking rates (SR) without including the effect of SR on PSC explicitly. Here we used long-term (30 yr) measured data of PSC and steer weight gain (SWG), extended with the help of a model for SR effect, to develop multiple-variable regression functions for predicting PSC and SWG across a wide range of SR (0.2–1.32 steers ha−1 for summer grazing season, June to mid-October) on a loam soil in a northern mixed-grass prairie. April to June rainfall was the primary weather variable influencing PSC (R2 = 0.45); inclusion of SR and soil water content on 1 April improved the accuracy in predicting PSC (R2 = 0.64). Combining the response of PSC to SR and the response of SWG to both PSC and SR enables ranchers to explore tradeoffs between economic net return and environmental impact (land conservation) as influenced by SR and weather variations. The result was further extended from the loam soil at the experimental site to the other two soil types (loam sandy and clay loam soils) by using a simple soil influence factor. A simple spreadsheet-based decision support tool can be developed to facilitate stocking decisions by ranchers in a northern mixedgrass prairie to adaptively manage rangelands in an effort to increase economic net return and reduce land degradation associated with high weather variability and SR levels. Abbreviations: DC, Drought Calculator; HPGRS, High Plains Grasslands Research Station; HPPSC, peak standing crop; GPFARM, Great Plains Framework for Agricultural Resource Management; PSC, peak standing crop; SR, stocking rate; SWG, steer weight gain; TDN, total intake digestible nutrient. Quan X. Fang Agronomy College, Qingdao Agricultural University, Changcheng Road 700, Chengyang District, Qingdao, Shandong, China, 266108. *Corresponding author (fangqx@igsnrr.ac.cn) L.R. Ahuja, USDA-ARS-NPA-ASRU 2150 Centre Ave., Bldg. D, Ste. 200 Fort Collins, CO, 80526 (laj.ahuja@ars. usda.gov) A.A. Andales, Department of Soil and Crop Sciences, Colorado State University, 1170 Campus Delivery, Fort Collins, CO 80523-1170 (Allan.Andales@colostate.edu). J.D. Derner, USDA-ARS, High Plains Grasslands Research Station, 8408 Hildreth Road, Cheyenne, WY 82009-8899 (Justin.Derner@ars.usda.gov) doi:10.2134/advagricsystmodel5.c7 Published December 5, 2014
Comparison of vergence mechanisms between university students with good and poor sleep quality.

AIM To compare the vergence mechanisms between good and poor sleepers in university students. METHODS A total of 64 university students were recruited in this study. The validated Malay version of Pittsburgh Sleep Quality Index questionnaire (PSQI-M) was used to measure the participants' sleep quality over the past month. Participants were categorized as good sleepers (n=32) and poor sleepers (n=32) based on the PSQI-M scores. Heterophoria and fusional vergences were measured at distance and near. Mann-Whitney U test was used to compare heterophoria, negative fusional vergence (NFV), and positive fusional vergence (PFV) at distance and near between good and poor sleepers. Spearman correlation analysis was used to study the relationship between PSQI-M score and PFV at distance. RESULTS Both distance and near heterophorias were not significantly different between good and poor sleepers (P>0.05). There was a difference in distance PFV (P<0.05) between good and poor sleepers, but not in distance NFV, near NFV, and near PFV (P>0.05). Distance PFV was negatively correlated with PSQI-M score (rs=-0.33, P<0.05). CONCLUSION University students with poor sleep quality demonstrates a reduced ability to maintain fusion with increasing convergence demand at distance. Sleep quality assessment during binocular vision examination in university students is recommended.
The Impact of Police Violence on Communities: Unpacking How Fatal Use of Force Infuences Resident Calls to 911 and Police Activity

A seminal piece in our understanding of how high-profle cases of police violence can affect communities, Desmond, Papachristos, and Kirk (2016), found that resident calls to the police via 911 significantly declined after the beating of Frank Jude. These effects were especially prevalent in primarily Black neighborhoods. In this study, we used an interrupted time series design to replicate the original results in a different city using a fatal incident of police violence. We also extended the methods of original study by further disaggregating the follow-up efects to include officer-initiated events, which capture more discretionary activity for patrol officers. Our results confirm the original findings, with resident calls to 911 declining in majority-Black neighborhoods after a deadly incident of police violence, signifying a decay in community trust and legitimacy. Importantly, we also fnd an immediate and striking decline in officer-initiated activity after the same incident in majority-Black neighborhoods. Conversely, White neighborhoods experienced a slight increase. This study reinforces and adds further context to a growing body of research that explains how incidents of police violence can affect the actions of community residents and the police, including how we conceptualize and measure the concept of “de-policing. ”
VARIABILITY OF SOME WINTER WHEAT TRAITS FROM BREEDING PROCESS

Za dobivanje genotipova željenih svojstava u postupku je oplemenjivanja izuzetno znacajno odabrati odgovarajuce roditelje za križanje. Da bi se mogao provesti odgovarajuci odabir potrebno je imati biljni materijal velike varijabilnosti na svojstva koja se žele oplemeniti. Kao roditelji u postupku oplemenjivanja mogu poslužiti i genotipovi koji se vec nalaze u oplemenjivacko-selekcijskom procesu, te je i njihova varijabilnost znacajna. Stoga su tijekom 1997. godine provedena ispitivanja varijabilnosti broja klasica u klasu, broja zrna u klasu i mase klasa na 34 genotipa iz oplemenjivackog programa Agrigeneticsa, s ciljem utvrđivanja varijabilnosti mjerenih svojstava i razlika između ispitivanih genotipova, te utvrđivanja razlika između ispitivanih genotipova i standardnih sorti Žitarke i Sane. Pokus je postavljen po slucajnom blok sustavu u cetiri ponavljanja na povrsini ekonomije Krnjak, zapadno od Donjeg Miholjca. Ispitivanje navedenih triju osobina klasa provedeno je u laboratoriju Poljoprivrednog fakulteta. Za svaki je genotip ispitano 200 klasova, 50 po svakom ponavljanju. Na osnovu rezultata mjerenja utvrđene su statisticki visoko opravdane razlike između ispitivanih genotipova, te između ispitivanih genotipova i standardnih sorti Žitarke i Sane. Rezultati mjerenja pokazali su znacajnu varijabilnost ispitivanih svojstava koja je, kao prvo, znacajna za buduce oplemenjivacke programe i stvaranje genotipova s boljim svojstvima od dosadasnjih, a kao drugo, daje mogucnost usmjeravanja oplemenjivackih programa u razlicitim pravcima. Na osnovu rezultata mjerenja za ispitivana su svojstva utvrđeni i koeficijenti korelacija. Jaka pozitivna korelacija postojala je između broja klasica u klasu i broja zrna po klasu (r = 0,62**), te broja klasica u klasu i mase zrna po klasu (r = 0,57**). Broj zrna u klasu bio je u veoma jakoj pozitivnoj korelaciji (r = 0,83**) s masom zrna po klasu.