Miracle-dz/UniFAR-FTUs huggingface dataset:
A prominent stepwise advance of the tree line in north‐east Finland

The elevational limit of trees (henceforth, the ‘tree line’) is widely considered to be a sensitive indicator of environmental change. Here, we document the 20th century tree line advance and increase in the tree population at the tree line ecotone, along a Pinus sylvestris‐dominated slope in north‐eastern Finland, in conditions where growth and recruitment have generally been linked to temperature variation. Using tree recruitment ages (growth to 1.3 m height) along an elevational transect, we compared recruitment to variation in environmental conditions associated with tree line dynamics, seed and cone crops, and reindeer densities. We further investigated the relationships among temperature and tree‐level growth variables. Results show the existence of a former tree line at approximately 400 m a.s. l. and an advance of trees that began in the 1920s and reached the top of the fell (at 470 m a.s.l.) in the 1980s. During this time, the population density of P. sylvestris increased from 4 to 468 trees within the 5.6 ha study plot. Needle and shoot lengths were positively related to air temperature but recruitment was not. Average rate of P. sylvestris advance over the 20th century was consistent with earlier studies, but the temporal patterns of both upslope advance and population density increase were unexpected: both were characterized by a strongly stepwise pattern, culminating in a rapid advance and density increase in the 1970–1980s, and returning to low levels in the 1990s. Despite a positive relationship between growth and temperature variables at the tree level, climatic variables, or seed and cone crops were inconsistent with recruitment patterns. For most part of the 20th century, the increase corresponded to the gradual atmospheric CO2 increase, but of the variables screened only the changes in reindeer densities coincided with the stepwise pattern. Synthesis. Our results confirmed the connection between tree‐level processes and temperature variability as expected from earlier studies. However, recruitment was not correlated with any of the environmental variables. Our findings point towards complex tree line dynamics, in which biotic agents may play a major role in mediating tree line response to environmental change.
Genotypic variation in the persistence of transgenerational responses to seasonal cues *

Phenotypes respond to environments experienced directly by an individual, via phenotypic plasticity, or to the environment experienced by ancestors, via transgenerational environmental effects. The adaptive value of environmental effects depends not only on the strength and direction of the induced response but also on how long the response persists within and across generations, and how stably it is expressed across environments that are encountered subsequently. Little is known about the genetic basis of those distinct components, or even whether they exhibit genetic variation. We tested for genetic differences in the inducibility, temporal persistence, and environmental stability of transgenerational environmental effects in Arabidopsis thaliana. Genetic variation existed in the inducibility of transgenerational effects on traits expressed across the life cycle. Surprisingly, the persistence of transgenerational effects into the third generation was uncorrelated with their induction in the second generation. Although environmental effects for some traits in some genotypes weakened over successive generations, others were stronger or even in the opposite direction in more distant generations. Therefore, transgenerational effects in more distant generations are not merely caused by the retention or dissipation of those expressed in prior generations, but they may be genetically independent traits with the potential to evolve independently.
Hexokinase 2 displacement from mitochondria‐associated membranes prompts Ca2+‐dependent death of cancer cells

Cancer cells undergo changes in metabolic and survival pathways that increase their malignancy. Isoform 2 of the glycolytic enzyme hexokinase (HK2) enhances both glucose metabolism and resistance to death stimuli in many neoplastic cell types. Here we observe that HK2 locates at mitochondria-endoplasmic reticulum (ER) contact sites called MAMs (Mitochondria-Associated Membranes). HK2 displacement from MAMs with a selective peptide triggers mitochondrial Ca2+ overload caused by Ca2+ release from ER via inositol-3-phosphate receptors (IP3Rs) and by Ca2+ entry through plasma membrane. This results in Ca2+-dependent calpain activation, mitochondrial depolarization and cell death. The HK2-targeting peptide causes massive death of chronic lymphocytic leukemia B cells freshly isolated from patients, and an actionable form of the peptide reduces growth of breast and colon cancer cells allografted in mice without noxious effects on healthy tissues. These results identify a signalling pathway primed by HK2 displacement from MAMs that can be activated as anti-neoplastic strategy.
Sambucus nigra L.

Deciduous shrub or more rarely a small tree to 10 m, often with straight, vigorous erect shoots from the base; branches often arching. Bark brownish-grey, deeply furrowed, corky. Branches containing a white, porous pith. Twigs stout, greyish, with prominent lenticels. Leaves pinnate; leaflets 3-(5-7)-9, 3-9 cm, ovate, ovate-lanceolate or ovate-elliptic; acuminate; serrate; sparingly hairy on veins beneath. Lower pair of leaflets with short stalk (4-5 mm), other leaflets sessile. Petiole 3-4 cm, deeply grooved on the adaxial surface; stipules 0 or very small and subulate. Axillary buds triangular, reddish, 2-3 mm. Foliage and young shoots foetid. Stalk-like extrafloral nectaries (5-10 mm x 1 mm) occur at the base of leaves and leaflets. Inflorescence flat-topped, 10-20 cm diameter, corymbose with 5 primary rays. Flowers 5-merous, actinomorphic; calyx limb very small; corolla rotate with short tube and flat spreading limb; 5 mm diameter, cream-white; fragrant. Anthers extrorse, cream. Style short, with 3-5 stigmas. Fruit a drupe, 6-8 mm, globose, black, rarely greenish, containing 3-5 compressed seeds (for seed sizes and weights, see section VIII(C)). Pollen grains pale yellow, ellipsoidal, densely tuberculated, 31 x 15-16 gm (Knuth Poll. II). Sambucus (Caprifoliaceae) is a genus of approximately 20 temperate and subtropical species of small trees, shrubs and herbs (Mabberley 1997). Bolli (1994) recognizes only nine, regarding S. maderensis Lowe, S. canadensis L. , S. palmensis Link, S. cerulea Raf. and S. peruviana Humboldt as subspecies of S. nigra. A large number of variants are known in horticulture (Bean 1951). Two forms have repeatedly been recorded as naturalized in Britain. The green-berried form viridis, also known asfructo-albo, leucocarpa and chlorocarpa, has been seen by the authors on Fleam Dyke, Cambridgeshire, in 1985 and again in 2001 and was recorded near Sheffield by Ardron & Rotherham (1984). A variety with deeply dissected leaflets (var. laciniata) is noted in a number of local floras (e.g. Wolley-Dod 1937; Lousley 1976). The inheritance of
Prophylactic Intra-Uterine β-Cyclodextrin Administration during Intra-Uterine Ureaplasma parvum Infection Partly Prevents Liver Inflammation without Interfering with the Enterohepatic Circulation of the Fetal Sheep

Chorioamnionitis can lead to inflammation and injury of the liver and gut, thereby predisposing patients to adverse outcomes such as necrotizing enterocolitis (NEC). In addition, intestinal bile acids (BAs) accumulation is causally linked to NEC development. Plant sterols are a promising intervention to prevent NEC development, considering their anti-inflammatory properties in the liver. Therefore, we investigated whether an intra-amniotic (IA) Ureaplasma parvum (UP) infection affected the liver and enterohepatic circulation (EHC) and evaluated whether an IA administered plant sterol mixture dissolved in β-cyclodextrin exerted prophylactic effects. An ovine chorioamnionitis model was used in which liver inflammation and the EHC were assessed following IA UP exposure in the presence or absence of IA prophylactic plant sterols (a mixture of β-sitosterol and campesterol dissolved in β-cyclodextrin (carrier)) or carrier alone. IA UP exposure caused an inflammatory reaction in the liver, histologically seen as clustered and conflated hepatic erythropoiesis in the parenchyma, which was partially prevented by IA administration of sterol + β-cyclodextrin, or β-cyclodextrin alone. In addition, IA administration of β-cyclodextrin prior to UP caused changes in the expression of several hepatic BAs transporters, without causing alterations in other aspects of the EHC. Thereby, the addition of plant sterols to the carrier β-cyclodextrin did not have additional effects.
Facial Expression Recognition Based on Weighted-Cluster Loss and Deep Transfer Learning Using a Highly Imbalanced Dataset

Facial expression recognition (FER) is a challenging problem in the fields of pattern recognition and computer vision. The recent success of convolutional neural networks (CNNs) in object detection and object segmentation tasks has shown promise in building an automatic deep CNN-based FER model. However, in real-world scenarios, performance degrades dramatically owing to the great diversity of factors unrelated to facial expressions, and due to a lack of training data and an intrinsic imbalance in the existing facial emotion datasets. To tackle these problems, this paper not only applies deep transfer learning techniques, but also proposes a novel loss function called weighted-cluster loss, which is used during the fine-tuning phase. Specifically, the weighted-cluster loss function simultaneously improves the intra-class compactness and the inter-class separability by learning a class center for each emotion class. It also takes the imbalance in a facial expression dataset into account by giving each emotion class a weight based on its proportion of the total number of images. In addition, a recent, successful deep CNN architecture, pre-trained in the task of face identification with the VGGFace2 database from the Visual Geometry Group at Oxford University, is employed and fine-tuned using the proposed loss function to recognize eight basic facial emotions from the AffectNet database of facial expression, valence, and arousal computing in the wild. Experiments on an AffectNet real-world facial dataset demonstrate that our method outperforms the baseline CNN models that use either weighted-softmax loss or center loss.
High-yield production of recombinant platelet factor 4 by harnessing and honing the gram-negative bacterial secretory apparatus

Platelet factor 4 is a cytokine released into the bloodstream by activated platelets where it plays a pivotal role in etiology and diagnosis of heparin-induced thrombocytopenia. Therefore, a sustainable source of recombinant PF4 with structural and functional similarity to its native form is urgently needed to be used in diagnostic procedures. To this end, a three-in-one primary construct was designed from which three secondary constructs can be derived each capable of employing either type I, type II secretory or cytoplasmic pathways. Protein expression and secretion were performed in Escherichia coli BL21 (DE3) and confirmed by SDS-PAGE and Western blotting. To further enhance protein secretion, the effect of several controllable chemical factors including IPTG, Triton X-100, sucrose, and glycine were individually investigated at the outset. In the next step, according to a fractional factorial approach, the synergistic effects of IPTG, Triton X-100, and glycine on secretion were further investigated. To ascertain the structure and function of the secreted recombinant proteins, dynamic light scattering was utilized to confirm the rPF4 tetramerization and heparin-mediated ultra-large complex formation. Moreover, Raman spectroscopy and Western blotting were exploited to evaluate the secondary and quaternary structures, respectively. The type II secretory pathway was proven to be superior to type I in the case of rPF4 secretion. Supplementation with chemical enhancers improved the protein secretion mediated by the Type II system to approximately more than 500 μg/mL. Large quantities of native rPF4 up to 20 mg were purified as the culture medium was scaled up to 40 mL. Western blotting confirmed the formation of dimers and tetramers in the secreted rPF4 proteins. Dynamic light scattering revealed the rPF4 oligomerization into of larger complexes of approximately 100–1200 nm in size following heparin supplementation, implying proper protein folding and tetramerization. Moreover, the rPF4 secondary structure was found to be 43.5% Random coil, 32.5% β-sheet, 18.6% α-helix and 4.9% Turn, which is in perfect agreement with the native structure. Our results indicate that the gram-negative type II bacterial secretory system holds a great promise as a reliable protein production strategy with industrial applications. However, further efforts are required to realize the full potential of secretory pathways regarding their application to proteins with distinct characteristics.
Comparison of different approaches to the study of local recruitment of breeders

Although the recruitment of breeders is as important to population dynamics as mortality, it has received far less attention from statisticians working at modelling capture histories of marked animals. However, two main approaches to studying local recruitment have become available in the last three years. Both deal with birds marked as chicks and then possibly resighted or recaptured only as breeders (the same approaches may be applied more generally whenever breeders and non-breeders can be distinguished in a population by working with the sole observations of breeding animals). This situation is natural to species of colonial birds sampled on the breeding site where the young remain away from the breeding site previous to their first breeding attempt. The first method published (Clobert et al., 1994) contrasts, in the context of a survival analysis, the capture rates of known breeders and the capture rates of animals up to their first observed breeding attempt. Young animals as a group are less likely .
A Method of Transmitting Known Numbers of Trypanosomes with a Note on the Numeric Relation of Trypanosomes to Infection

This method for transmitting trypanosomes was evolved during chemotherapeutic researches in which several species of these parasites were used as the test organism, by reason of the necessity for having a fairly accurate, rapid, and simple means of infecting rats with known numbers of trypanosomes. As will be pointed out later in this paper, the time of true incubation of trypanosomes following infection by the intraperitoneal route, as well as to some extent the duration of the animal's life, are factors influenced by the numbers of trypanosomes injected; or, even more important, as will be discussed in a later paper, is the fact that the parasitropic effects of a drug or substance under study and the resistance of the animal to the drug's organotropic effects are apparently modified, to some extent at least, by whether the animal was infected with small or large numbers of trypanosomes. While it is necessary to use a parasite of sufficient aggressiveness and vitality to yield definite results and indicate any therapeutic action of the agent under study, yet it is possible to mask the finer grades of therapeutic effects by an overwhelming infection, or, on the other hand, lose or vitiate an. experiment by infecting with too few parasites. With these practical considerations in mind, I have worked out a method for transmitting approximately known numbers of trypanosomes, which has proved comparatively simple, fairly accurate, and very useful. By this method, it is possible to infect a large series of rats with any desired number of trypanosomes, in a sterile manner, and without sacrificing the seed animal. It is highly desirable, especially in chemotherapeutic researches, to infect the animals with a uniform number of parasites, not only the animals of a single series, but likewise those of different series, and this method has been found to fulfill this important requirement satisfactorily.
Homology modeling identifies crucial amino-acid residues that confer higher Na+ transport capacity of OcHKT1;5 from Oryza coarctata Roxb.

HKT1;5 loci/alleles are important determinants of crop salinity tolerance. HKT1;5s encode plasmalemma-localized Na+-transporters, retrieving xylem Na+ into xylem parenchyma cells, reducing shoot Na+ accumulation. Allelic variation in rice OsHKT1;5 sequence in specific landraces (Nona Bokra OsHKT1;5-NB/Nipponbare OsHKT1;5-Ni) correlates with variation in salt tolerance. Oryza coarctata, a halophytic wild rice, grows in fluctuating salinity at the seawater-estuarine interface in Indian and Bangladeshi coastal regions. The distinct transport characteristics of the shoots and roots expressing O. coarctata OcHKT1;5 transporter, are reported vis-à-vis OsHKT1;5-Ni. Yeast sodium extrusion-deficient cells expressing OcHKT1;5 are sensitive to increasing Na+ (10-100 mM). Electrophysiological measurements in Xenopus oocytes expressing O. coarctata or rice HKT1;5 transporters indicates that OcHKT1;5, like OsHKT1;5-Ni is a Na+-selective transporter, but displays 16-fold lower affinity for Na+ and 3.5-fold higher maximal conductance than OsHKT1;5-Ni. For Na+ concentrations greater than 10 mM, OcHKT1;5 conductance is higher than that of OsHKT1;5-Ni, indicating potential of OcHKT1;5 for increasing domesticated rice salt tolerance. Homology modeling/ simulation suggests that four key amino acid changes in OcHKT1;5 (in loops on the extracellular side; E239K, G207R, G214R, L363V), account for its lower affinity and higher Na+ conductance vis-à-vis OsHKT1;5-Ni. Of these, E239K in OcHKT1;5, confers lower affinity for Na+ transport, as evidenced by Na+ transport assays of reciprocal site directed mutants for both transporters (OcHKT1;5- K239E, OsHKT1;5-Ni- E270K) in Xenopus oocytes. Both transporters have analogous roles in xylem sap desalinization and differences in Na+ transport affinity/ conductance between the transporters is attributable to differences in xylem sap Na+ concentrations in both species.
Localization of nif genes on large plasmids in Rhizobium galegae

Plasmid DNA of six strains of Rhizobium galegae was blotted onto nitrocellulose and hybridized with the 4.8 kb PstI fragment of pRme4lb, a megaplasmid carrying the nifH and the nifD genes of Rhizobium meliloti. DNA sequences homologous to the nif genes were localized on the megaplasmid or on the large plasmid bands of the R. galegae strains tested. In three of the strains analysed the nif genes were located on the megaplasmids. In the other three strains investigated, which also possessed megaplasmids, the nif genes were located on the smaller plasmids.
Comparison of the AIMS65 score with the Glasgow-Blatchford and Rockall scoring systems for the prediction of the risk of in-hospital death among patients with upper gastrointestinal bleeding.

OBJECTIVE the aim of this study was to compare the AIMS65, Glasgow-Blatchford score (GBS) and Rockall score for the prediction of the risk of in-hospital death among patients with upper gastrointestinal bleeding (UGIB). METHODS patients with UGIB admitted to the ZhongDa hospital from June 2015 to July 2017 were retrospectively collected. All patients were assessed by the AIMS65, GBS and Rockall score and the main outcomes were in-hospital mortality. Odds ratios (OR) and 95 % confidence interval (CI) were estimated to assess the association of the three scores with the risk of death using logistic regression models. Subsequently, their risk stratification accuracy were compared. Finally, their predictive power was compared using the area under the receiver operating characteristic curve (AUROC). RESULTS of the 284 UGIB patients enrolled in the study, 51 (18.0 %) had variceal bleeding (VUGIB) and 10 patients (3.5 %) died. AIMS65 (OR = 5.14, 95 % CI = 2.48, 10.64), GBS (OR = 1.66, 95 % CI = 1.28, 2.15) and Rockall (OR = 2.72, 95 % CI = 1.76, 4.18) scores were positively associated with death risk among all patients. The AIMS65 score (high-risk group vs low-risk group: 11.9 % vs 0.0 %, p < 0.001) was effective to classify high-risk in-hospital deaths populations. The AIMS65 score was the best approach to predict in-hospital death among all UGIB patients (AUROC: AIMS65 0.955, GBS 0.882, Rockall 0.938), NVUGIB patients (AUROC = 0.969, 95 % CI = 0.937, 0.989) or VUGIB patients (AUROC = 0.885, 95 % CI = 0.765, 0.967). CONCLUSIONS the AIMS65 score is the most convenient UGIB prognostic score to predict in-hospital mortality and may be more suitable for patients with NVUGIB.
Effect of sucrose on activity of starch synthesis enzymes in rice ears in culture

Grain filling of rice (Oryza sativa L.) is thought to be affected not only by the supply of carbohydrate from source organs, but also by sink activity, including the activities of enzymes related in starch synthesis. To examine the effect of translocated carbohydrate on sink activity, we cultured detached ears (cut 7 days after flowering) in a solution containing sucrose at various concentrations, glutamine and vitamins. Grain weights 16 days after the start of ear culture increased with increasing sucrose concentration up to 50-70 g sucrose l -1 , but not above this range, probably because of low water potential. Activities of ADP glucose pyrophosphorylase, soluble starch synthase and sucrose synthase rapidly decreased in grains grown without sucrose, but increased with increasing sucrose concentration up to 50-70 g l -1 . Expression of mRNAs for these enzymes and for sucrose transporter was also generally increased by sucrose at 50-70 g l -1 . Though there was a good correlation between activity and expression of mRNA for sucrose synthase, the correlation for other enzymes was not very good. Thus, we suggested that the sink activity of grains in rice ears, and therefore the grain filling, was affected by the supply of carbohydrate from source organs, and that it was also owing to factors other than transcriptional regulation.
Design Rule of Mach-Zehnder Interferometer Sensors for Ultra-High Sensitivity

A design rule for a Mach-Zehnder interferometer (MZI) sensor is presented, allowing tunable sensitivity by appropriately choosing the MZI arm lengths according to the formula given in this paper. The present MZI sensor designed by this method can achieve an ultra-high sensitivity, which is much higher than any other traditional MZI sensors. An example is given with silicon-on-insulator (SOI) nanowires and the device sensitivity is as high as 106 nm/refractive-index -unit (or even higher), by choosing the MZI arms appropriately. This makes it possible for one to realize a low-cost optical sensing system with a detection limit as high as 10−6 refractive-index-unit, even when a cheap optical spectrum analyzer with low-resolution (e.g., 1 nm) is used for the wavelength-shift measurement.
RSVdb: a comprehensive database of transcriptome RNA structure

RNA fulfills a crucial regulatory role in cells by folding into a complex RNA structure. To date, a chemical compound, dimethyl sulfate (DMS), has been developed to probe the RNA structure at the transcriptome level effectively. We proposed a database, RSVdb (https://taolab.nwafu.edu.cn/rsvdb/), for the browsing and visualization of transcriptome RNA structures. RSVdb, including 626 225 RNAs with validated DMS reactivity from 178 samples in eight species, supports four main functions: information retrieval, research overview, structure prediction and resource download. Users can search for species, studies, transcripts and genes of interest; browse the quality control of sequencing data and statistical charts of RNA structure information; preview and perform online prediction of RNA structures in silico and under DMS restraint of different experimental treatments and download RNA structure data for species and studies. Together, RSVdb provides a reference for RNA structure and will support future research on the function of RNA structure at the transcriptome level.