Miracle-dz/UniFAR-FTUs huggingface dataset:
Correction of Potassium Fertigation Rate of Apple Tree (Malus domestica Borkh.) in Central Russia during the Growing Season

The proper use of potassium fertilizer can stimulate a significant yield increase. However, the application of excessively high rates of potassium can reduce the availability of soil calcium for apple trees. The potassium fertigation rate must meet the apple tree’s requirements so that the applied fertilizers can be absorbed by the roots as much as possible. Crop load in apple orchards sometimes varies significantly in different years. The potassium content in apple fruits is relatively high, and the maximum requirement for this nutrient occurs when fruits grow and ripen. Different crop loads at that time mean the various demands of trees and need for changing application rates for this nutrient. The investigation was carried out in the experimental orchard of I.V. Michurin Federal Scientific Centre (Michurinsk, Russia) in 2016 and 2017 (52.885131, 40.465613). We studied seasonal changes of potassium and calcium contents in soil, fruits, and leaves and their relationship with yield during the research. We paid much attention to the potassium rate shift on its content in leaves and fruits and cultivars “Lobo” and “Zhigulevskoye” yield. If the potassium application rate changes according to the actual crop load, it stimulates the yield growth or (if the crop load was relatively low) the reduction of the rate did not lower the productivity. Moreover, we studied the relationship between potassium and calcium nutrition. The decrease in potassium fertigation rate increased the availability of soil calcium. It was the reason for fruit calcium concentration enlargement and mitigation of the K/Ca ratio. We also specified some parameters for soil–leaf diagnosis for potassium nutrition during the growing season.
Influence of electro-ejaculator on serum concentrations of acute phase proteins and bone metabolism biomarkers in male dromedary camels (Camelus dromedarius)

ABSTRACT This study was carried out to evaluate the effect of electroejaculation (EEJ) on the serum concentrations of the acute phase proteins (APPs) serum amyloid A (SAA) and haptoglobin (Hp), and on the bone metabolism biomarkers osteocalcin (OC), bone-specific alkaline phosphatase (b-ALP) and pyridinoline cross-links (PYD). Twenty sexually mature apparently healthy male camels were assigned to EEJ. Parallel, 8 naturally mated male camels were enrolled as a control group. Three blood samples were collected from each camel: just before (T0), directly after (T1) and 24 h after (T2) EEJ or natural mating camels. The serum concentrations of the APPs and bone biomarkers were determined. The serum concentrations of SAA increased significantly at T1 compared to T0. In none of the 2 groups was the serum concentration of Hp differed significantly. The serum concentrations of OC increased significantly at T1 compared to T0. In none of the 2 groups was the serum concentration of b-ALP differed significantly among T0, T1 and T2. It is concluded that acute phase reaction, manifested by significant increases of SAA, had occurred in male camels as a result of EEJ. In addition, EEJ increased serum concentration of the bone formation biomarker OC.
Hearing Loss–Related Issues Affecting Quality of Life in Preschool Children

Objective The impact of hearing loss (HL) on quality of life (QOL) in young children has not been examined systematically. The objective of this study was to examine patient, parent, and professional perspectives on experiences and situations that affect the QOL in young children with HL and to identify themes that emerged from coded data to develop a parent-proxy QOL measure for young children with HL. Study Design Qualitative study with 6 focus groups followed by semistructured interviews with other parents and professionals as stakeholder checks. Setting Academic medical center and local schools for the deaf. Methods Audiology department clinic lists were used to identify eligible participants, who included 5- to 7-year-old children with permanent HL and parents of 2- to 7-year-old children with permanent HL. A sample of 6 children and 12 parents participated in focus groups. An audiology department and multiple schools for the deaf in the area were contacted to recruit for professional participants, resulting in a sample of 10 professionals who participated in focus groups. Focus groups and interviews were audiotaped and transcribed verbatim. Inductive thematic analysis of focus group transcripts identified key concepts and emerging themes of how HL affects young children. Results Six themes emerged from the data: behavior, feelings, environments, social/activities, family, and hearing equipment. Child, parent, and professional focus group themes overlapped well, and data saturation was reached. Conclusion These qualitative data provided insight into HL-related issues affecting young children’s QOL and were used to create items for a new parent-proxy QOL questionnaire.
Rapid Target Binding and Cargo Release of Activatable Liposomes Bearing HER2 and FAP Single-Chain Antibody Fragments Reveal Potentials for Image-Guided Delivery to Tumors

Liposomes represent suitable tools for the diagnosis and treatment of a variety of diseases, including cancers. To study the role of the human epidermal growth factor receptor 2 (HER2) as target in cancer imaging and image-guided deliveries, liposomes were encapsulated with an intrinsically quenched concentration of a near-infrared fluorescent dye in their aqueous interior. This resulted in quenched liposomes (termed LipQ), that were fluorescent exclusively upon degradation, dye release, and activation. The liposomes carried an always-on green fluorescent phospholipid in the lipid layer to enable tracking of intact liposomes. Additionally, they were functionalized with single-chain antibody fragments directed to fibroblast activation protein (FAP), a marker of stromal fibroblasts of most epithelial cancers, and to HER2, whose overexpression in 20–30% of all breast cancers and many other cancer types is associated with a poor treatment outcome and relapse. We show that both monospecific (HER2-IL) and bispecific (Bi-FAP/HER2-IL) formulations are quenched and undergo HER2-dependent rapid uptake and cargo release in cultured target cells and tumor models in mice. Thereby, tumor fluorescence was retained in whole-body NIRF imaging for 32–48 h post-injection. Opposed to cell culture studies, Bi-FAP/HER2-IL-based live confocal microscopy of a high HER2-expressing tumor revealed nuclear delivery of the encapsulated dye. Thus, the liposomes have potentials for image-guided nuclear delivery of therapeutics, and also for intraoperative delineation of tumors, metastasis, and tumor margins.
Screening of proteins interacting with ERF transcriptional factor from Populus simonii × P.nigra by yeast two-hybrid method

ABSTRACT To investigate the biology functions of ERF transcriptional factor in Populus simonii × P.nigra, the proteins interacting with ERF were screened by the yeast two-hybrid method. The bait vector harbouring ERF and cDNA library of Populus simonii × P.nigra were constructed. The bait had no self-activation and toxicity to yeast cells in the yeast two-hybrid system. The library titering experiment indicated that it could meet the requirement for the yeast two-hybrid library screen. Five proteins that interacted with ERF were obtained, including galactinol-sucrose galactosyl transferase 2, phosphoinositide-specific phospholipase C family protein, MLP-like protein, senescence-associated protein and an unknown protein. Real-time polymerase chain reaction showed that the expression levels of ERF and five interacting protein genes increased after salt treatment. Gene ontology analysis associated most of the interacting proteins with stress response. These results showed that ERF might share similar function with these proteins and they act together to regulate the salt response of Populus simonii × P.nigra. This study provided experimental evidence for further revealing the biological function of the ERF transcription factor in poplar.
Single Planting Creates Expanding Naturalized Population of Quercus palustris Far From Its Native Range Limit

abstract Ornamental plant species are frequently planted well outside of their native ranges and, in some cases, escape from cultivation to develop naturalized populations. Understanding the causes and consequences of naturalization resulting from intra-continental introductions will shed light both on mechanisms of invasion and on the potential for facilitated migration as a response to global climate change. In this study, we characterized a naturalized population of pin oak (Quercus palustris) that has recently arisen in the woodlands of Colby College in central Maine, 275 km from its native range limit. The population stemmed from trees in two small horticultural plantings, one from 1950 and one from the mid-1980′s. As an initial indication of potential invasiveness, we compared growth rates of individual pin oak trees to those of red oak (Quercus rubra), the most closely related native species and likely competitor. We also carried out genetic testing to determine how many parents gave rise to the naturalized population. Growth rates of pin oak saplings were only marginally greater than those of red oak saplings. Genetic analysis showed that at least 75% of sampled progeny descended from the six trees of the original 1950 population, with at least one-third of the progeny descending from two individual trees. Our results demonstrate that a small number of founders can be sufficient to establish a naturalized population beyond the native range limit. It is too soon to tell whether naturalized populations of pin oak in Maine will behave invasively, as might be expected with a trans-oceanic introduction, or will behave more similarly to populations at a naturally expanding range limit. There is no evidence to date that the naturalized pin oak population is detrimentally impacting the native forest community.
Sequence Braiding: Visual Overviews of Temporal Event Sequences and Attributes

Temporal event sequence alignment has been used in many domains to visualize nuanced changes and interactions over time. Existing approaches align one or two sentinel events. Overview tasks require examining all alignments of interest using interaction and time or juxtaposition of many visualizations. Furthermore, any event attribute overviews are not closely tied to sequence visualizations. We present S<sc>equence</sc> B<sc>raiding,</sc> a novel overview visualization for temporal event sequences and attributes using a layered directed acyclic network. S<sc>equence</sc> B<sc>raiding</sc> visually aligns many temporal events and attribute groups simultaneously and supports arbitrary ordering, absence, and duplication of events. In a controlled experiment we compare S<sc>equence</sc> B<sc>raiding</sc> and IDMVis on user task completion time, correctness, error, and confidence. Our results provide good evidence that users of S<sc>equence</sc> B<sc>raiding</sc> can understand high-level patterns and trends faster and with similar error. A full version of this paper with all appendices; the evaluation stimuli, data, and analysis code; and source code are available at <inline-formula><tex-math notation="LaTeX">$\text{osf.io}/\mathrm{mq}2\mathrm{wt}$</tex-math><alternatives><graphic position="float" orientation="portrait" xlink:href="27tvcg02-bartolomeo-3030442-eqinline-1-small.tif"/></alternatives></inline-formula>.
Multiscale cardiac imaging spanning the whole heart and its internal cellular architecture in a small animal model

Cardiac pumping depends on the morphological structure of the heart, but also on its subcellular (ultrastructural) architecture, which enables cardiac contraction. In cases of congenital heart defects, localized ultrastructural disruptions that increase the risk of heart failure are only starting to be discovered. This is in part due to a lack of technologies that can image the three-dimensional (3D) heart structure, to assess malformations; and its ultrastructure, to assess organelle disruptions. We present here a multiscale, correlative imaging procedure that achieves high-resolution images of the whole heart, using 3D micro-computed tomography (micro-CT); and its ultrastructure, using 3D scanning electron microscopy (SEM). In a small animal model (chicken embryo), we achieved uniform fixation and staining of the whole heart, without losing ultrastructural preservation on the same sample, enabling correlative multiscale imaging. Our approach enables multiscale studies in models of congenital heart disease and beyond.
Phosphoproteomics Meets Chemical Genetics: Approaches for Global Mapping and Deciphering the Phosphoproteome

Protein kinases are important enzymes involved in the regulation of various cellular processes. To function properly, each protein kinase phosphorylates only a limited number of proteins among the thousands present in the cell. This provides a rapid and dynamic regulatory mechanism that controls biological functions of the proteins. Despite the importance of protein kinases, most of their substrates remain unknown. Recently, the advances in the fields of protein engineering, chemical genetics, and mass spectrometry have boosted studies on identification of bona fide substrates of protein kinases. Among the various methods in protein kinase specific substrate identification, genetically engineered protein kinases and quantitative phosphoproteomics have become promising tools. Herein, we review the current advances in the field of chemical genetics in analog-sensitive protein kinase mutants and highlight selected strategies for identifying protein kinase substrates and studying the dynamic nature of protein phosphorylation.
Bifidobacterium alters the gut microbiota and modulates the functional metabolism of T regulatory cells in the context of immune checkpoint blockade

Significance Many millions of people take probiotics over the counter, but very little is known about what they do and whether they really work. Here we show that in mice, introducing Bifidobacterium, one of the most commonly used probiotics, not only colonizes the gut, but also alters the entire microbiotic landscape. We previously found that this treatment rescues mice from an otherwise fatal inflammatory syndrome brought on by anti–CTLA-4 antibody, a checkpoint inhibitor that often causes autoimmunity in humans undergoing cancer treatment. Here we show that this is effect is due, at least in part, to the effect of this probiotic treatment on regulatory CD4+ cells, whose metabolic and immune suppressive functions are altered. These CD4+ regulatory T cells are known to be a key mechanism in the control of autoreactivity in the immune system in both mice and humans. Thus, we found a direct connection between probiotic treatment and one of the known principal mechanisms for controlling excess immune responses. Immune checkpoint-blocking antibodies that attenuate immune tolerance have been used to effectively treat cancer, but they can also trigger severe immune-related adverse events. Previously, we found that Bifidobacterium could mitigate intestinal immunopathology in the context of CTLA-4 blockade in mice. Here we examined the mechanism underlying this process. We found that Bifidobacterium altered the composition of the gut microbiota systematically in a regulatory T cell (Treg)-dependent manner. Moreover, this altered commensal community enhanced both the mitochondrial fitness and the IL-10–mediated suppressive functions of intestinal Tregs, contributing to the amelioration of colitis during immune checkpoint blockade.
Nonhistone Proteins HMGB1 and HMGB2 Differentially Modulate the Response of Human Embryonic Stem Cells and the Progenitor Cells to the Anticancer Drug Etoposide

HMGB1 and HMGB2 proteins are abundantly expressed in human embryonic stem cells (hESCs) and hESC-derived progenitor cells (neuroectodermal cells, hNECs), though their functional roles in pluripotency and the mechanisms underlying their differentiation in response to the anticancer drug etoposide remain to be elucidated. Here, we show that HMGB1 and/or HMGB2 knockdown (KD) by shRNA in hESCs did not affect the cell stemness/pluripotency regardless of etoposide treatments, while in hESC-derived neuroectodermal cells, treatment resulted in differential effects on cell survival and the generation of rosette structures. The objective of this work was to determine whether HMGB1/2 proteins could modulate the sensitivity of hESCs and hESC-derived progenitor cells (hNECs) to etoposide. We observed that HMGB1 KD knockdown (KD) and, to a lesser extent, HMGB2 KD enhanced the sensitivity of hESCs to etoposide. Enhanced accumulation of 53BP1 on telomeres was detected by confocal microscopy in both untreated and etoposide-treated HMGB1 KD hESCs and hNECs, indicating that the loss of HMGB1 could destabilize telomeres. On the other hand, decreased accumulation of 53BP1 on telomeres in etoposide-treated HMGB2 KD hESCs (but not in HMGB2 KD hNECs) suggested that the loss of HMGB2 promoted the stability of telomeres. Etoposide treatment of hESCs resulted in a significant enhancement of telomerase activity, with the highest increase observed in the HMGB2 KD cells. Interestingly, no changes in telomerase activity were found in etoposide-treated control hNECs, but HMGB2 KD (unlike HMGB1 KD) markedly decreased telomerase activity in these cells. Changes in telomerase activity in the etoposide-treated HMGB2 KD hESCs or hNECs coincided with the appearance of DNA damage markers and could already be observed before the onset of apoptosis. Collectively, we have demonstrated that HMGB1 or HMGB2 differentially modulate the impact of etoposide treatment on human embryonic stem cells and their progenitor cells, suggesting possible strategies for the enhancement of the efficacy of this anticancer drug.
Ferulic acid (FA) protects human retinal pigment epithelial cells from H2O2‐induced oxidative injuries

The aim of present study is to investigate whether Ferulic acid (FA), a natural polyphenol antioxidant, was able to protect ARPE‑19 cells from hydrogen peroxide (H2O2)‑induced damage, and elucidate the underlying mechanisms. Our results revealed that FA pre‐treatment for 24 hours can reverse cell loss of H2O2‐induced ARPE‐19 cells via the promotion of cell proliferation and prevention of apoptosis, as evidenced by 5‐ethynyl‐2′‐deoxyuridine (EdU) incorporation and terminal deoxynucleotidyl transferase‐mediated dUTP nick end‐labelling (TUNEL) assay, respectively. Moreover, the addition of FA (5 mM) can decrease Bax and cleaved caspase‐3 protein expression, but increase Bcl‐2 protein expression in ARPE‐19 cells. Furthermore, H2O2‐induced oxidative stress in ARPE‐19 cells was significantly alleviated by FA, illustrated by reduced levels of ROS and MDA. In addition, the attenuated antioxidant enzymes activities of (SOD, CAT and GPX) and GSH level were reversed almost to the normal base level by the pre‐addition of FA for 24 hours. In all assays, FA itself did not exert any effect on the change of the above parameters. These novel findings indicated that FA effectively protected human ARPE‐19 cells from H2O2‐induced oxidative damage through its pro‐proliferation, anti‐apoptosis and antioxidant activity, suggesting that FA has a therapeutic potential in the prevention and treatment of AMD.
Smell your self: Olfactory stimulation improves self-concept in Alzheimer’s disease

ABSTRACT Research has demonstrated a link between decline in autobiographical memory and decline in the sense of self in Alzheimer’s disease (AD). Recent work has also shown that odour is a powerful cue to alleviate decline in autobiographical memory in AD. Based on these findings, we investigated whether odour exposure improves access to self-concept in AD patients. To this end, we invited AD and control participants to make self-related statements (i.e., statements in response to the question “Who am I? ”) after odour exposure or without odour exposure. We measured the number and the categories of self-related statements (i.e., whether these statements described the psychological, social or physical self) that were generated in each condition. Results demonstrated that both AD and control participants generated more self-statements in the odour condition than in the odor-free condition, especially psychological self-statements. This study is the first to demonstrate the positive influence of olfactory stimulation on the retrieval of self-related knowledge in AD.
Detection and identification of azithromycin resistance mutations on Treponema pallidum 23S rRNA gene by nested multiplex polymerase chain reaction

Background: Azithromycin-resistant strains of Treponema pallidum is associated with the mutation of 23S rRNA gene of T. pallidum. Although these strains are now prevalent in many countries, there is no laboratory test kit to detect and identify these mutations. Thus, in this study we developed a nested multiplex polymerase chain reaction (PCR) to detect and identify A2058G and A2059G mutations in 23S rRNA gene. Methods: Three primer sets were designed for nested PCR reactions. To obtain maximum PCR reaction, all parameters were optimized. The specificity of the primer sets was evaluated towards some microorganisms. A sensitivity test was conducted to get detection limit of deoxyribonucleic acid (DNA). Forty-five whole blood specimens were tested by PCR, and positive results were confirmed by the DNA sequencing. Results: The assay could detect at least 4,400 DNA copy number and showed no cross reaction with other microorganisms used in the specificity test. A total 13 of 45 whole blood specimens were PCR positive for T. pallidum, and no single mutations (either A2058G or A2059G) were detected. Two positive specimens were confirmed by the DNA sequencing and showed no mutation. Conclusion: Nested multiplex PCR developed in this study showed a specific and sensitive test for the detection and identification of A2058G and/or A2059G mutations of 23S rRNA T. pallidum gene.