Miracle-dz/UniFAR-FTUs huggingface dataset:
Dry Matter Production in a Tomato Crop: Measurements and Simulation

Abstract Simulation of dry matter production by the explanatory glasshouse crop growth model SUKAM (Gijzen, 1992, Simulation Monographs), based on SUCROS87 (Spitters, Van Keulen and Van Kraalingen, 1989, Simulation and systems management in crop protection), was validated for tomato. In the model, assimilation rates are calculated separately for shaded and sunlit leaf area at different cumulative leaf area in the canopy, taking into account the different interception of direct and diffuse components of light. Daily crop gross assimilation rate (Pgd) is computed by integration of these rates over total crop leaf area and over the day. Leaf photochemical efficiency and potential gross assimilation rate at saturating light depend on temperature and CO2 concentration and are approximated as being identical in the whole canopy. Crop growth results from Pgd minus maintenance respiration rate (Rm; dependent on temperature and crop dry weight), multiplied by the conversion efficiency (carbohydrates to structural dry matter; Cf). Growth experiments (periodic destructive harvest) with different planting dates and plant densities and two data-sets from commercially grown crops, were used for model validation. Hourly averages for global radiation outside the glasshouse, glasshouse temperature and CO2 concentration, together with measured leaf area index, dry matter distribution (for calculation of Cf) and organ dry weights (for calculation of Rm) were the inputs to the model. Dry matter production (both level and dynamic behaviour) was simulated reasonably well for most experiments, but final dry matter production was under-estimated by about 27% for the commercially grown crops. At low irradiance and with large crop dry weight, growth rate was under-estimated, probably as a result of over-estimation of Rm. This could almost completely explain the large under-estimation for the commercially grown crops, which had large dry weight. Final dry matter production was over-estimated by 7-11% if daily averages instead of hourly input of climatic data were used. It is concluded that SUKAM is a reliable model for simulating dry matter production in a tomato crop, except for those situations where Rm has a large influence on crop growth rate (low irradiance and large crop dry weight). An improved estimate of Rm would take into account the influence of metabolic activity. A preliminary attempt to relate maintenance costs to relative growth rate (a measure for metabolic activity), showed promising results.
Antiherpetic in vitro activity of Gamochaeta simplicicaulis extract

Aqueous extracts of Gamochaeta simplicicaulis present true antiviral activity in vitro against different members of the herpesvirus family (herpes simplex virus types 1 and 2, human cytomegalovirus, bovine herpes virus and lower activity with pseudorabies virus). The extract had no activity against some RNA (naked and enveloped) viruses and adenoviruses. The extract was not virucidal but its antiviral index (AI) was high enough to justify further analysis. Different experimental approaches indicate that an early step of viral replication, at least the adsorption period, was involved in the antiviral activity.
Artificial light at night amplifies seasonal relapse of haemosporidian parasites in a widespread songbird

Urban habitats can shape interactions between hosts and parasites by altering not only exposure rates but also within-host processes. Artificial light at night is common in urban environments, and chronic exposure can impair host immunity in ways that may increase infection. However, studies of causal links between this stressor, immunity, and infection dynamics are rare, particularly in migratory animals. Here, we experimentally tested how artificial light at night affects cellular immunity and haemosporidian parasite intensity across the annual cycle of migrant and resident subspecies of the dark-eyed junco (Junco hyemalis). We monitored an experimental group exposed to light at night and a control group under natural light/dark cycles as they passed through short days simulating early spring to longer days simulating the breeding season, followed by fall migration. Using generalized additive models, we show that artificial light at night increased inflammation, and leukocyte counts were greatest in early spring and fall. At the start of the experiment, few birds had active infections based on microscopy, but PCR revealed many birds had chronic infections. Artificial light at night increased parasitemia across the annual cycle, with strong peaks in spring and fall that were largely absent in control birds. As birds were kept in indoor aviaries to prevent vector exposure, this increased parasitemia indicates relapse of chronic infection during costly life history stages (i.e., reproduction). Although the immunological and parasitological time series were in phase for control birds, cross-correlation analyses also revealed artificial light at night desynchronized leukocyte profiles and parasitemia, which could suggest a general exaggerated inflammatory response. Our study shows how a common anthropogenic influence can shape within-host processes to affect infection dynamics.
The Loss of the Inverted Repeat in the Putranjivoid Clade of Malpighiales

The typical plastid genome (plastome) of photosynthetic angiosperms comprises a pair of Inverted Repeat regions (IRs), which separate a Large Single Copy region (LSC) from a Small Single Copy region (SSC). The independent losses of IRs have been documented in only a few distinct plant lineages. The majority of these taxa show uncommonly high levels of plastome structural variations, while a few have otherwise conserved plastomes. For a better understanding of the function of IRs in stabilizing plastome structure, more taxa that have lost IRs need to be investigated. We analyzed the plastomes of eight species from two genera of the putranjivoid clade of Malpighiales using Illumina paired-end sequencing, the de novo assembly strategy GetOrganelle, as well as a combination of two annotation methods. We found that all eight plastomes of the putranjivoid clade have lost their IRB, representing the fifth case of IR loss within autotrophic angiosperms. Coinciding with the loss of the IR, plastomes of the putranjivoid clade have experienced significant structural variations including gene and intron losses, multiple large inversions, as well as the translocation and duplication of plastome segments. However, Balanopaceae, one of the close relatives of the putranjivoid clade, exhibit a relatively conserved plastome organization with canonical IRs. Our results corroborate earlier reports that the IR loss and additional structural reorganizations are closely linked, hinting at a shared mechanism that underpins structural disturbances.
Linear Neural Parsing and Hybrid Enhancement for Enhanced Universal Dependencies

To accomplish the shared task on dependency parsing we explore the use of a linear transition-based neural dependency parser as well as a combination of three of them by means of a linear tree combination algorithm. We train separate models for each language on the shared task data. We compare our base parser with two biaffine parsers and also present an ensemble combination of all five parsers, which achieves an average UAS 1.88 point lower than the top official submission. For producing the enhanced dependencies, we exploit a hybrid approach, coupling an algorithmic graph transformation of the dependency tree with predictions made by a multitask machine learning model.
Clinical-Coder: Assigning Interpretable ICD-10 Codes to Chinese Clinical Notes

In this paper, we introduce Clinical-Coder, an online system aiming to assign ICD codes to Chinese clinical notes. ICD coding has been a research hotspot of clinical medicine, but the interpretability of prediction hinders its practical application. We exploit a Dilated Convolutional Attention network with N-gram Matching mechanism (DCANM) to capture semantic features for non-continuous words and continuous n-gram words, concentrating on explaining the reason why each ICD code to be predicted. The experiments demonstrate that our approach is effective and that our system is able to provide supporting information in clinical decision making.
Clarifying the Tooth-Derived Stem Cells Behavior in a 3D Biomimetic Scaffold for Bone Tissue Engineering Applications

Massive amounts of cell are needed for creating tissue engineered 3D constructs, which often requires culture on scaffolds under dynamic conditions to facilitate nutrients and oxygen diffusion. Dynamic cultures are expected to improve cell viability and proliferation rate, when compared to static conditions. However, cells from distinct types and/or tissues sources may respond differently to external stimuli and be incompatible with culture under mechanical shear stress. The first aim of this work was to show that dental stem cells are a valuable source for improving bone regeneration potential of artificial grafts. Mesenchymal stem/stromal cells (MSCs) were isolated from human dental follicle (hDFMSC) and pulp tissues (hDPMSC) and shown to express prototypical stem cell markers. The follicle and pulp dental MSCs capacity to differentiate into osteoblast lineage was evaluated after seeding on 3D porous scaffolds of collagen-nanohydroxyapatite/phosphoserine biocomposite cryogel with osteogenic factors in the culture medium. Both tooth-derived MSCs were able to show high ALP activity, express osteogenic gene markers and secrete osteopontin (OPN). Thereafter, designed multicompartment holder adaptable to spinner flasks was used for dynamic culture (50 rpm) of both dental MSCs types within the porous 3D scaffolds. Standard static culture conditions were used as control. Culture under dynamic conditions promoted follicle MSCs proliferation, while improving their spatial distribution within the scaffold. Under dynamic conditions, the biocomposite scaffold promoted MSCs osteogenic differentiation, as suggested by increased alkaline phosphatase (ALP) activity, higher osteogenic gene expression and OPN deposition. In a similar manner, under dynamic conditions, dental pulp MSCs also showed higher ALP activity and proliferation rate, but lower amounts of osteopontin secretion, when compared to static conditions. After implantation, dental follicle MSCs-loaded 3D scaffolds cultured under dynamic conditions showed higher tissue ingrowth and osteogenic differentiation (higher human OPN secretion) than dental pulp cells. Overall, this study explored the use of tooth-derived stem cells as a clinical alternative source for bone tissue engineering, together with an innovative device for dynamic culture of cell-laden 3D scaffolds. Results showed that human MSCs response upon culture on 3D scaffolds, depends on the cells source and the culture regimen. This suggests that both the type of cells and their culture conditions should be carefully adjusted according to the final clinical application.
Dynamics of ovarian follicles in Tupinambis merianae lizards

Follicular dynamics of Tupinambis merianae lizards was analyzed by means of ultrasound examination and radio frequency identification, during three con- secutive reproductive periods, both in reproduction and in sexual isolation. Series of follicular development which ended in ovulation, and series of follicular develop - ment without ovulation, followed by a regression process, were observed, as well as a combination of both. Ovulation was found to be strongly dependent on mating con- summation. In 34% of the cases in which follicular development ended with ovula- tion, and hence oviposition, follicles showed a steady and uniform growth up to the periovulatory period, also acquiring a mild echogenicity. In the absence of ovulation (66% of cases), follicular development showed two patterns: a short and a long-term anovulatory follicular cycle. In the first pattern, follicles showed limited growth and a non-echoic aspect, which suggests a previtellogenic condition. In the second pattern, follicles exhibited a growth and echogenicity similar to periovulatory ones, presum- ably attaining a vitellogenic stage. In addition, follicular development in reproduc - ing females was superior to that of sexually isolated females. Follicular development, ovulation, and follicular regression appeared to constitute generalized events affecting most, if not all, of the recruited follicles.
Heating technology for malignant tumors: a review

Abstract The therapeutic application of heat is very effective in cancer treatment. Both hyperthermia, i.e., heating to 39–45 °C to induce sensitization to radiotherapy and chemotherapy, and thermal ablation, where temperatures beyond 50 °C destroy tumor cells directly are frequently applied in the clinic. Achievement of an effective treatment requires high quality heating equipment, precise thermal dosimetry, and adequate quality assurance. Several types of devices, antennas and heating or power delivery systems have been proposed and developed in recent decades. These vary considerably in technique, heating depth, ability to focus, and in the size of the heating focus. Clinically used heating techniques involve electromagnetic and ultrasonic heating, hyperthermic perfusion and conductive heating. Depending on clinical objectives and available technology, thermal therapies can be subdivided into three broad categories: local, locoregional, or whole body heating. Clinically used local heating techniques include interstitial hyperthermia and ablation, high intensity focused ultrasound (HIFU), scanned focused ultrasound (SFUS), electroporation, nanoparticle heating, intraluminal heating and superficial heating. Locoregional heating techniques include phased array systems, capacitive systems and isolated perfusion. Whole body techniques focus on prevention of heat loss supplemented with energy deposition in the body, e.g., by infrared radiation. This review presents an overview of clinical hyperthermia and ablation devices used for local, locoregional, and whole body therapy. Proven and experimental clinical applications of thermal ablation and hyperthermia are listed. Methods for temperature measurement and the role of treatment planning to control treatments are discussed briefly, as well as future perspectives for heating technology for the treatment of tumors. Graphical Abstract Schematic overview of clinically proven heating techniques used for various indications and tumor locations.
CASIA’s System for IWSLT 2020 Open Domain Translation

This paper describes the CASIA’s system for the IWSLT 2020 open domain translation task. This year we participate in both Chinese→Japanese and Japanese→Chinese translation tasks. Our system is neural machine translation system based on Transformer model. We augment the training data with knowledge distillation and back translation to improve the translation performance. Domain data classification and weighted domain model ensemble are introduced to generate the final translation result. We compare and analyze the performance on development data with different model settings and different data processing techniques.
Effect of foliar application of calcium and boron on growth, productivity and quality of Indian gooseberry (Emblica officinalis)

An experiment was conducted in ‘NA7’ cultivar of Indian gooseberry (Emblica officinalis Gaertn) to assess whether pre-harvest foliar application of Ca (as calcium carbonate), B (as borax) individually or their combination influences physiological problems (poor fruit set, blossom and fruit drop, deformation of fruits etc.), fruit yield and quality or not. Treatments consisted of Ca as CaCO3 at 0.2%, 0.4%, 0.6%, boron as borax at 0.2%, 0.4% 0.6%, Ca+B (mixed) 0.2%, 0.4%, 0.6% and plants sprayed with water served as the control. Treatments were applied five times on full grown tree of Indian gooseberry cultivar ‘NA7’ at pre bloom, full bloom, at fruit set initiation, pea stage (fruit development stage) and pre-harvest stage (one month before harvest). Results indicated that fruit harvested from plants which were sprayed with Ca+B 0.4% had significantly lesser incidence of fruit deformation (0.8%), blossom and fruit drop (32.6%) than in the plants kept under control (2.8% and 79.2%, respectively). The maximum yield (158.6 kg/tree) was recorded with the application of calcium carbonate + borax 0.4%, while minimum was recorded under control (105.2 kg/tree). In totality all the treatments have increased the fruit weight, fruit size, number of fruit/shoot, and quality of fruits as compared to control. The maximum dry matter (20.2%), juice content (78.5%), vitamin C (626.49 mg/100 g) was recorded with calcium carbonate + borax 0.4%. Similarly, it was also observed that such fruit (sprayed with Ca+B 0.4%) were bold, had slightly higher TSS (16.5%) at harvest than those in control (15.1%). Studies indicated that preharvest foliar application of Ca+B is quite useful for reducing the incidence of physiological problems and getting higher marketable yield in ‘NA7’ Indian gooseberry. Ca+B 0.4% significantly increased fruit size, fruit length and breadth. Calcium carbonate at concentration of 0.4% significantly reduced the fruit drop and increased the retention of blossom and deformed fruit.
Impact of transgenic potatoes expressing anti‐bacterial agents on bacterial endophytes is comparable with the effects of plant genotype, soil type and pathogen infection

1. Blackleg and soft rot disease of potatoes Solanum tuberosum L. , mainly caused by the bacterial pathogen Erwinia carotovora ssp. atrospetica (Eca), lead to enormous yield losses world-wide. Genetically modified (GM) potatoes producing anti-bacterial agents, such as cecropin/attacin and T4 lysozyme, may offer effective future pathogen control strategies. Because of concerns about undesirable ecological side-effects of GM crops, it is important to analyse the potential environmental impact of GM crops carefully. The objective of this study was to investigate the effect of GM potatoes with anti-bacterial activity on the diversity and functional abilities of bacteria colonizing the intercellular spaces and vascular tissues (endosphere) of potato plants. 2. A greenhouse experiment was performed to analyse the effect of GM potatoes expressing either attacin/cecropin or T4 lysozyme on endophytic bacterial communities. Endophytic bacteria colonizing the GM potato lines as well as their nearly isogenic wild types were analysed at two vegetation stages. In order to compare GM-related variations with impacts caused by changing environmental conditions, potatoes were cultivated in two different soil types, and challenged with the pathogen Eca. Endophytic diversity was assessed by 16S rRNA-based terminal-restriction fragment length polymorphism (T-RFLP) analysis. Cultivated community members were identified by 16S rRNA gene analysis and screened for a range of plant growth-promoting and plant pathogen-antagonistic abilities. 3. Both genetic transformation events induced a differentiation in the community structures of associated bacterial populations and in the related functional abilities of cultivated bacterial endophytes. In comparison with the other factors analysed, the impact of both genetic modification types was minor or comparable with the variations caused by plant genotype, vegetation stage, pathogen exposure and soil type. 4. Synthesis and applications. This study has shown that the expression of anti-bacterial proteins may affect bacterial endophytes; however, the impacts were no greater than those of other factors analysed. Future risk assessment studies of GM crops should consider different environmental factors. This study contributes to the ongoing risk assessment of GM crops and provides valuable baseline information for prospective GM crop assays.
Synthesizing Systems Biology Knowledge from Omics Using Genome‐Scale Models

Omic technologies have enabled the complete readout of the molecular state of a cell at different biological scales. In principle, the combination of multiple omic data types can provide an integrated view of the entire biological system. This integration requires appropriate models in a systems biology approach. Here, genome‐scale models (GEMs) are focused upon as one computational systems biology approach for interpreting and integrating multi‐omic data. GEMs convert the reactions (related to metabolism, transcription, and translation) that occur in an organism to a mathematical formulation that can be modeled using optimization principles. A variety of genome‐scale modeling methods used to interpret multiple omic data types, including genomics, transcriptomics, proteomics, metabolomics, and meta‐omics are reviewed. The ability to interpret omics in the context of biological systems has yielded important findings for human health, environmental biotechnology, bioenergy, and metabolic engineering. The authors find that concurrent with advancements in omic technologies, genome‐scale modeling methods are also expanding to enable better interpretation of omic data. Therefore, continued synthesis of valuable knowledge, through the integration of omic data with GEMs, are expected.
Memory deficits in Sprague Dawley rats with spontaneous ventriculomegaly

Spontaneous ventriculomegaly has been observed in rats that were presumed normal. Because the external phenotype of these animals is unremarkable, they can be inadvertently included in behavioral experiments, despite the considerable enlargement of the ventricular system, reduced cortical thickness, and hippocampal atrophy upon imaging. Given the role of such structures in memory consolidation, we evaluated long‐term memory retention while decision making in rats with spontaneous ventriculomegaly.
Effectiveness of Multidimensional Controllers Designated to Steering of the Motions of Ship at Low Speed

The article described two full multidimensional controllers applied to steer a real vessel named ‘Blue Lady’ that is used by the Foundation for Safety of Navigation and Environment Protection at its training and research facility loacted at Silm lake in Poland. Both controllers were based on different approaches, but finally gave similar results. The first part describes the object to be controlled which is a training ship used for training of navigators in various conditions, areas and manoeuvres. This is followed by a short description of the theory for both controllers, Robust and Linear Matrix Inequalities (LMI). Next real time trials are described, which are 3 different manouvers for low velocities, executed by both LMI and Robust contrllers. In these trials ‘Blue Lady’ velocities, silhouete trajectory ans wind data are recorded. Finally the quality of work for both controllers is collected in two tables.
Patient acceptance of using telemedicine for follow-up of lupus nephritis in the COVID-19 outbreak

We read with interest the preliminary German Society of Rheumatology recommendations for the management of patients with autoimmune inflammatory rheumatic diseases during the COVID-19 pandemic, which highlighted the importance of weighing the infection risk of doctor visits against the risk of missing disease controls in individual cases.1 Indeed, the attendance of our lupus nephritis clinic dropped by 14.4% in the 8-week period after the outbreak compared with the same time last year based on the citywide computerised Clinical Management System (So H, 2020). Those unattended patients were at risk of disease flares, which would lead to damage accrual, but at the same time, the rest were exposed to the threat of COVID-19.2 As the other national body suggested, the use of telemedicine (TM), also known as telehealth, to reduce potential exposure to severe acute respiratory syndrome coronavirus 2 might be a reasonable option in these patients.3 Since this is a shared decision-making process between patients and rheumatology healthcare providers, we conducted an online survey to analyse the patient acceptance and perceptions regarding …