Miracle-dz/UniFAR-FTUs huggingface dataset:
Detecting the genetic basis of local adaptation in loblolly pine (Pinus taeda L.) using whole exome‐wide genotyping and an integrative landscape genomics analysis approach

Abstract In the Southern United States, the widely distributed loblolly pine contributes greatly to lumber and pulp production, as well as providing many important ecosystem services. Climate change may affect the productivity and range of loblolly pine. Nevertheless, we have insufficient knowledge of the adaptive potential and the genetics underlying the adaptability of loblolly pine. To address this, we tested the association of 2.8 million whole exome‐based single nucleotide polymorphisms (SNPs) with climate and geographic variables, including temperature, precipitation, latitude, longitude, and elevation data. Using an integrative landscape genomics approach by combining multiple environmental association and outlier detection analyses, we identified 611 SNPs associated with 56 climate and geographic variables. Longitude, maximum temperature of the warm months and monthly precipitation associated with most SNPs, indicating their importance and complexity in shaping the genetic variation in loblolly pine. Functions of candidate genes related to terpenoid synthesis, pathogen defense, transcription factors, and abiotic stress response. We provided evidence that environment‐associated SNPs also composed the genetic structure of adaptive phenotypic traits including height, diameter, metabolite levels, and gene transcript abundance. Our study promotes understanding of the genetic basis of local adaptation in loblolly pine and provides promising tools for selecting genotypes adapted to local environments in a changing climate.
Mesoscopic free energy as a framework for modeling shape memory alloys

This article presents a reinterpretation of the one-dimensional shape memory alloy model by Müller, Achenbach, and Seelecke (M-A-S) that offers extended capabilities and a simpler formulation. The cornerstone of this model is a continuous, multi-well free energy that governs phase change at a mesoscopic material scale. The free energy has been reformulated to allow asymmetric tensile and compressive behavior as well as temperature-dependent hysteresis while maintaining the necessary smoothness conditions. The free energy is then used to derive expressions for latent heat coefficients that include the influence of stress, the difference in stiffness between the phases, and irreversibility. Special attention is devoted to the role of irreversibility and latent heat predictions, which are compared to experimental measurements. The new model also includes an updated set of kinetics equations that operate on the convexity of the energy wells instead of the height of the energy barriers. This modification eliminates several sets of equations from the overall formulation without any compromises in performance and also bypasses limitations of the barrier-based equations.
Effect of inclusion conditions on characteristics of spray dried whey protein hydrolysate/γ-cyclodextrin complexes

Whey protein hydrolysate (WPH) has functional food potential. However, the bitter taste and high hygroscopicity of WPH may limit its application to use as food ingredients. To reduce the shortcomings of WPH, it was encapsulated by γ -cyclodextrin ( γ -CD) as inclusion complexes. The aim of this work was to study the effect of inclusion conditions on the various properties of spray dried inclusion complex of WPH/ γ - cyclodextrin. Effects of incubation temperature (20-50 ° C), incubation time (3-9 hr) and mixing ratio between γ -CD and WPH (20:80, 40:60 and 60:40) were studied. Spray drying of WPH/ γ -CD inclusion complexes were operated at an inlet temperature of 180 ° C to produce the encapsulated WPH powder. The properties of encapsulated WPH powder including moisture content, bulk density, particle size distribution, solubility, morphology, color values, surface hydrophobicity, bitterness and hygroscopicity were investigated. It was found that all of encapsulated WPH showed the better properties than non-encapsulated WPH, especially hygroscopicity and bitterness. The hygroscopicity of encapsulated WPH reduced in the range of 27.42% to 57.67%, bitterness reduced in the range of 51.61% to 89.78% compared to that of non-encapsulated WPH. For the incubation time effect, moisture content and bitterness score of encapsulated WPH decreased with decreasing of incubation time. The incubation temperature did not significantly affect on various properties of encapsulated WPH. For the effect of ratio between WPH and γ -CD, higher content of γ -CD led to lower values of hygroscopicity and bitterness score. From the results in this study, encapsulation of WPH by inclusion method and spray drying improve the characteristics of whey protein hydrolysate used as food ingredients in a variety of food products.
SENYAWA ANTIMIKROBA YANG DIHASILKAN OLEH BAKTERI ASAM LAKTAT ASAL BEKASAM

Bakteri asam laktat (BAL) adalah mikroba dominan yang ditemukan dalam fermentasi ikan. Tujuan penelitian ini adalah menentukan perkiraan kuantitatif awal dari substansi antimikroba yang dihasilkan oleh isolat BAL asal bekasam dan mengetahui aktivitas antimikrobnya terhadap lima bakteri patogen. Perkiraan kuantitatif asam laktat dan H 2 O 2 , menggunakan metode titrasi. Uji aktivitas antimikroba menggunakan metode difusi sumur agar. Karakterisasi (morfologi, fisologi dan pertumbuhan) dan identifikasi menggunakan API 50 CHL (Bio-Mereux, France). Produksi asam laktat dan H 2 O 2 meningkat dengan waktu inkubasi untuk semua isolat kecuali pada isolat BP(3). Produksi asam laktat tertinggi adalah 21,765 g/L yang dihasilkan oleh isolat SK(5) (48 jam inkubasi). Konsentrasi H 2 O 2 yang dihasilkan oleh semua isolat jauh lebih rendah dibandingkan dengan asam laktat. Konsentrasi H 2 O 2 tertinggi ialah 0,079 g/L pada isolat BI(3) dan BP(20) dalam 72 jam inkubasi. Supernatan bebas sel yang dinetralkan tidak menghambat pertumbuhan bakteri uji, sedangkan yang tidak dinetralkan dapat mengambat bakteri uji yang digunakan dengan zona hambat 9 -15 mm. Zona penghambatan terbesar dihasilkan oleh isolat SK(5) (24 jam inkubasi) terhadap S. aureus . Isolat BI(3), BP(3) dan BP(20) adalah Pediococcus pentosaceus 1 dengan kemiripan sebesar 99,9%. Isolat SK(5) adalah Lactobacillus plantarum 1 dengan kemiripan sebesar 99,9%. Penelitian ini menunjukkan bahwa isolat BAL asal bekasam dapat dijadikan sebagai kandidat biopreservatif pangan terutama untuk pengolahan hasil perikanan. Kata kunci: antimikrobial, asam laktat, bakteri asam laktat, bekasam, dan hidrogen peroksida.
In Situ Forming, Dual-Crosslink Network, Self-Healing Hydrogel Enabled by a Bioorthogonal Nopoldiol–Benzoxaborolate Click Reaction with a Wide pH Range

The use of click chemistry as a hydrogel cross-linking reaction is often limited by slow reaction rates and harsh conditions, such as exposure to UV light and/or use of nonspecific or toxic reagents. On the other hand, the process of boronic ester formation between arylboronic acids and diols suffers from its intrinsic reversibility and low binding affinity at low pH, which impede its potential in many biomedical applications where a fast and stable click reaction is needed. Herein, we report a new concept of click hydrogel fabrication that combines a traditional sugar-based boronic ester and a novel nopoldiol-based benzoxaborolate as a dual-crosslink network (DCN) system. The cooperation of dynamic and rigid networks and the unique sensitivity of benzoxaborolate cross-links toward stimulus provide an intelligent hydrogel with a set of interesting features: (i) catalyst/light-free nopoldiol–benzoxaborolate bioorthogonal click cross-linking, (ii) rapid in situ formation within 26 s, (iii) wide self-healing.
‘Navelina’ sweet orange trees on five rootstocks in Northern Parana state, Brazil

Abstract Studies on rootstocks and scions are of major importance for citrus crop production. The goal of this study was to evaluate vegetative growth, yield performance, and fruit quality of ‘Navelina’ sweet orange trees grafted on five different rootstocks in Northern Parana state, Brazil. The experimental design was completely randomized blocks, with six replications, two plants per plot, and five treatments: ‘Rangpur’ lime; ‘Cleopatra’ mandarin, ‘Sunki’ mandarin; ‘Swingle’ citrumelo; and ‘Fepagro C-13’ citrange. Tree vegetative growth, yield performance, and fruit physical-chemical characteristics were analyzed. ‘Sunki’ mandarin provided the largest canopy volume for ‘Navelina’ sweet orange trees, whereas ‘Swingle’ citrumelo, ‘Fepagro C-13’ citrange, and ‘Rangpur’ lime provided a smaller volume for tree canopy. Compared to Rangpur lime, ‘Swingle’ citrumelo provided higher accumulated yield and production efficiency for ‘Navelina’ sweet orange trees. All rootstocks induced good physical and chemical quality to ‘Navelina’ sweet orange fruits.
IMPACT OF CLINICAL MASTITIS IN DAIRY FARMING AT KESHABPUR UPAZILLA IN JESSORE IN BANGLADESH

The study was conducted at upazilla veterinary hospital, Keshabpur, Jessore during the period of March 2013 to August 2013 to estimate the impact of clinical mastitis in dairy cows. Clinical mastitis was diagnosed on the basis of clinical signs and strip cup test (SCT). A total of 432 cases of dairy animals were recorded among them 65 cases were mastitis. The overall prevalence of mastitis was 15.05%. The prevalence of mastitis was 12.04% and 3.01% in cows and does respectively. In doe, the prevalence was 7.14% in Jamunapari goat and 4.46% in Black Bengal goat. Reproductive stages enhanced the prevalence of mastitis. The prevalence of mastitis was also significantly affected by floor conditions where 10.42% in cows and 8.04% in does in the farms with brick-block floor and 6.51% in cows and 3.57% in does with soil floor. The efficacy of Ceftriaxone and amoxicillin was better than gentamicin and streptomycin. Hygienic condition showed lower prevalence of mastitis 1.63% and 1.79% in cow and does respectively than the unhygienic farm.
Enteric protozoa of dogs: prevalence, associated risk factors and owners’ awareness in and around Hawassa town, Ethiopia

Dogs are reservoirs of zoonotic pathogens and pose a significant health risk to humans in most parts of the world. A cross sectional study design was used to estimate the prevalence of enteric protozoal parasites in dogs, to assess the associated risk factors and the level of owners’ awareness about zoonotic implications of enteric protozoa parasites in selected subcities of Hawassa town from October 2015 to June 2016. A total of 340 faecal samples were collected and examined for enteric protozoa using flotation techniques. Of these, 171 (50.3%) dogs were infected with one or more genera of enteric protozoa parasites. The parasites identified were Sarcocyst (28.5%), Isospora (20.6%), Cryptosporidium (8.5%), Neospora (8.2%) and Giardia (5.6%). About 34.5% of the examined dogs were infected with two to four enteric protozoa parasites. The overall prevalence of enteric protozoa parasites was significantly higher in younger dogs (χ 2 = 20.21, p < 0.05), semi-confined (χ 2 = 5.63, p < 0.05) and stray dogs (χ 2 = 23.01, p < 0.05). The prevalence of Sarcocyst (χ 2 = 14.45, p< 0.05), Isospora (χ 2 = 4.38, p < 0.05) and Neospora (χ 2 = 4.31, p < 0.05) was significantly higher in stray dogs as compared to owned dogs. Most of respondents and dog owners’ (76.5%), had no awareness on zoonotic enteric protozoa parasites of dogs. But 32.8% and 23.2% the respondents’ children hug and play with dogs, respectively. Most of them (71.7%) feed their dogs with uncooked butcher leftover and/or offals. About 66.2% of them dispose of dogs’ feces with garbage. Therefore, extension works for public education to improve public awareness on parasitic zoonoses, is very helpful to reduce the problem to the possible minimum level. Moreover, a close collaboration between veterinarians and public health professionals is highly helpful. Keywords: Dogs; Enteric protozoa; Ethiopia; Hawassa; Risk factors; Zoonotic
An ecosystem model of the global ocean including Fe, Si, P colimitations

Observations have shown that large areas of the world ocean are characterized by lower than expected chlorophyll concentrations given the ambient phosphate and nitrate levels. In these High Nutrient‐Low Chlorophyll regions, limitations of phytoplankton growth by other nutrients like silicate or iron have been hypothesized and further evidenced by in situ experiments. To explore these limitations, a nine‐component ecosystem model has been embedded in the Hamburg model of the oceanic carbon cycle (HAMOCC5). This model includes phosphate, silicate, dissolved iron, two phytoplankton size fractions (nanophytoplankton and diatoms), two zooplankton size fractions (microzooplankton and mesozooplankton), one detritus and semilabile dissolved organic matter. The model is able to reproduce the main characteristics of two of the three main HNLC areas, i.e., the Southern Ocean and the equatorial Pacific. In the subarctic Pacific, silicate and phosphate surface concentrations are largely underestimated because of deficiencies in ocean dynamics. The low chlorophyll concentrations in HNLC areas are explained by the traditional hypothesis of a simultaneous iron‐grazing limitation: Diatoms are limited by iron whereas nanophytoplankton is controlled by very efficient grazing by microzooplankton. Phytoplankton assimilates 18 × 109 mol Fe yr−1 of which 73% is supplied by regeneration within the euphotic zone. The model predicts that the ocean carries with it about 75% of the phytoplankton demand for new iron, assuming a 1% solubility for atmospheric iron. Finally, it is shown that a higher supply of iron to surface water leads to a higher export production but paradoxically to a lower primary productivity.
Chemokines in Lung Cancer

This review highlights the importance of CXC chemokine ligands and receptors in nonsmall cell lung cancer (NSCLC) with regard to tumor-associated angiogenesis, “immunoangiostasis,” and metastasis to specific organs. Chemokines are chemotactic cytokines that, in the context of cancer, appear to be important in either promoting tumor growth, tumor-associated angiogenesis, and metastasis or in inhibiting tumor growth through attenuation of tumor-associated angiogenesis. In addition, chemokines have been shown to promote tumor-targeted immunity and are also important in directing metastases to specific organs. Targeting chemokines may therefore ultimately be important as a clinical strategy in NSCLC.
The Impact of CYP2A6 Genotype on Smoking Cessation in an Extended Nicotine Patch Therapy Clinical Trial

We investigated the efficacy of standard (8-week nicotine, 16-week placebo) vs extended (24-week nicotine) patch therapy for smoking cessation, and the effect of slow nicotine metabolism, indicated by CYP2A6 reduced metabolizer (RM) genotype or low 3hydroxycotinine/cotinine ratio (3HC/COT), on abstinence. RM versus normal genotype predicted lower 3HC/COT. Extended vs standard treatment produced higher abstinence at 24 weeks (32% vs 20%), but not at 52 weeks (both 14%). Low 3HC/COT and RM genotype predicted higher abstinence on extended versus standard treatment at 24 (47% vs 25%, 38% vs 17%) and 28 weeks (34% vs 19%, 23% vs 11%), while high 3HC/COT or normal genotype did not. Within extended treatment, low versus high 3HC/COT predicted higher abstinence at 8 (48% vs 29%), 24 (47% vs 25%), and 28 weeks (34% vs 16%), with similar trends for the genotype effect. Overall, extending nicotine treatment increased abstinence during therapy, particularly for slow
Non-linear codes and concatenated codes for unequal error protection

We will present two different error control schemes for unequal error protection. Based on a general lower bound on the word error rate (WER) for the coded transmission of redundant data over discrete memoryless channels, the distance profile of the optimum error correcting code can be derived. This distance profile may serve as a basis for code construction as it is done by an approach applying a systematic computer search to the code construction which yields a non-linear code. The construction as well as decoding of the code is quite complex, hence, the length of the codewords is limited. The other approach combines concatenated Reed-Muller codes with iterative 'turbo' decoding techniques resulting in a powerful coding scheme suitable for unequal error protection (UEP). This facilitates the construction of very long codes from simpler shorter codes, since the decoding complexity depends only on the applied component codes. But compared to the first method the codes are less flexible as far as the design of the distance profile is concerned.
Chimeric antigen receptor preparation from hybridoma to T-cell expression

Abstract The successful use of chimeric antigen receptor (CAR) for hematological cancer treatment has influenced the direction taken in translational research toward an increasing focus on personalized targeted immunotherapy. Thus, a growing number of labs worldwide are now interested in testing their old antibody collections in this format to broaden the spectrum of utility and improve safety and efficacy. We herein present a straightforward protocol for the identification of an antibody from a hybridoma and the design of the single chain fragment that will be placed on the extracellular part of the CAR construct. We further show how to test the expression and the activity of the construct in primary T cells. We illustrate our demonstration with two new CARs targeted against the B cell receptor, more precisely the light chains κ and λ, that represent potential alternatives to the CD19 CAR used in the treatment of B-cell malignancies.
Enhancement of the Antibacterial Efficiency of Silver Nanoparticles against Gram-Positive and Gram-Negative Bacteria Using Blue Laser Light

Silver nanoparticles (Ag-NPs) possess excellent antibacterial properties and are considered to be an alternative material for treating antibiotic-resistant bacteria. The present study was aimed at enhancing the antibacterial efficiency of Ag-NPs using visible laser light against Escherichia coli and Staphylococcus aureus in vitro. Four concentrations of Ag-NPs (12.5, 25, 50, and 100 μg/ml), synthesized by the chemical reduction method, were utilized to conduct the antibacterial activity of prepared Ag-NPs. The antibacterial efficiencies of photoactivated Ag-NPs against both bacteria were determined by survival assay after exposure to laser irradiation. The mechanism of interactions between Ag-NPs and the bacterial cell membranes was then evaluated via scanning electron microscopy (SEM) and reactive oxygen species analysis to study the cytotoxic action of photoactivated Ag-NPs against both bacterial species. Results showed that the laser-activated Ag-NP treatment reduced the surviving population to 14% of the control in the E. coli population, while the survival in the S. aureus population was reduced to 28% of the control upon 10 min exposure time at the concentration of 50 μg/ml. However, S. aureus showed lower sensitivity after photoactivation compared to E. coli. Moreover, the effects depended on the concentration of Ag-NPs and exposure time to laser light. SEM images of treated bacterial cells indicated that substantial morphological changes occurred in cell membranes after treatment. The results suggested that Ag-NPs in the presence of visible light exhibit strong antibacterial activity which could be used to inactivate harmful and pathogenic microorganisms.
CALL on hold: The delayed benefits of an online workbook on L2 vocabulary learning

This study examines the effects of an online workbook and a paper workbook on L2 vocabulary acquisition. Participants consisted of 549 L2 learners of Spanish enrolled in a large language program at an American state university. The participants received 4 hours of classroom instruction per week and worked with an online or a paper workbook once a week during two semesters. They also completed a screening test and four vocabulary tests: two during the first semester and two during the second semester. The results showed no significant differences between the online and the paper workbook groups after one semester of instructional treatment. However, the online workbook group proved better than the paper workbook group in the second semester. These findings confirm results of previous studies on the beneficial role of CALL on L2 vocabulary acquisition, and they point to the pedagogical advantages of online workbooks for large language programs as long as enough length of exposure to the online environment is allotted.
Crossing Among Sixteen Sweet Potato Parents for Establishing Base Populations Breeding

The base - population of the controlled cross breeding is one of the important factors to develop a new improved cultivar. Since the incompatible nature of sweet potato remains a barrier for genetic improvement, therefore it requires a lot of crossed pairs. This study aimed to determine the level of incompatibility among crossing line between high yielding and micronutrient content cultivars. The field experiment conducted at Brawijaya University Research Station, Jatikerto-Malang, during February to August 2015. The North Carolina Design II was applied to sixty pairs controlled cross breeding and their sixty reciprocal pairs of six cultivars for micronutrient content enrichment with ten high yielding cultivars. The observations were made to the cross flowers number, capsules, fruit sets, and seeds number. The level of incompatibility between crossed pairs was determined by the level of fruit set. The result showed that most pairs were compatible (fruit set > 20%) and only few were incompatible (fruit set < 10%). Among six parents with micronutrient content enrichment, two of them, have a high compatibility as as female parents, to all the high yielding cultivars, i.e. BIS OP-61 and Cangkuang. Positioning as a female parent can improve the effectiveness of its selection scheme.
Effect of Electric Fields on the Rheological Properties of the Isotropic Phase of phic/p-Xylene Solutions

Abstract The effect of high ac electric fields upon a liquid crystalline polymer solution, poly(n-hexyl isocyanate) in p-xylene, is examined. The results show that the solutions exhibit an increase in rheological properties proportional to the strength of the field at concentrations well below those exhibiting liquid crystalline behavior. The effects of frequency and field strength are examined as a means to explain this previously unreported phenomenon.
Integrated Fault-Tolerant Control for Close Formation Flight

This paper investigates the position-tracking and attitude-tracking control problem of close formation flight with vortex effects under simultaneous actuator and sensor faults. On the basis of the estimated state and fault information from unknown input observers and relative output information from neighbors, an integration of decentralized fault estimation and distributed fault-tolerant control is developed to deal with bidirectional interactions and to guarantee the asymptotic stability and <inline-formula><tex-math notation="LaTeX">$H_\infty$</tex-math></inline-formula> performance of close formations.