Miracle-dz/UniFAR-FTUs huggingface dataset:
Membrane lipid domains and membrane lipid domain preparations: are they the same thing?

膜脂質ドメインに関する初期の考えは，人工膜に基づいた実験モデルと，調節された条件で細胞の界面活性剤処理によって得られた細胞ライセートを密度勾配遠心することによって調製された膜画分の研究から主に導かれた。 これらの研究によって，ゴルジ体がタンパク質を選別し，「ラフト」（スフィンゴ糖脂質，スフィンゴミエリン，セラミドそしてコレステロールに富んだ膜脂質ドメイン）を介してそれらを細胞膜へと輸送するという生物学的概念が導入された。 この概念は，この 10 年間に進化，発展してきたが，今や様々な実験的アプローチによって，こうしたドメインをインタクトな細胞で観察することも可能になってきた。 ここでは，細胞膜に存在するものと，我々が研究室の試験管の中で細胞膜から調製できるものとをきちんと区別することの必要性について議論する。
Size and visibility of Baltic cod eggs with reference to size‐selective and stage dependent predation mortality

Size of Baltic cod eggs from incubation experiments and from field samples was determined by microscopic analysis. Results from plankton samples were compared with corresponding size distributions of cod eggs found in herring stomachs. The influence of fixation on size of different developmental stages was studied. Live eggs from incubation experiments were also sized repeatedly throughout the developmental period with an optical plankton counter (OPC) based on light attenuance measurements as this was assumed to be more closely related to the visibility of the eggs for potential predators than egg diameter as obtained by microscopic analysis. Preservation in formaldehyde solution caused a small reduction in egg diameter (2.2%) whereby no differences between the developmental stages were detected. Egg size decreased slightly during incubation (6.9%) while the OPC measurements revealed a substantial increase in light attenuance during egg development (42.2%). In the field, a general decrease in egg size with increasing depth was observed while no change between the developmental stages was detectable. The mean size of eggs ingested by herring was slightly lower than in the water column which was most pronounced for the late stages containing a well-developed embryo. The frequency of eggs in an advanced stage of development was considerably higher in the stomachs than in corresponding plankton samples. Therefore, it is suggested that the selection of further developed egg stages by predatory fish in the central Baltic Sea, i.e. herring and sprat, is due to an increase of visibility during egg development in relation to growth and pigmentation of the embryo. Thus it is likely that egg mortality due to predation is stage-dependent rather than strictly size-selective.
Squeezing the most out of existing literature: a systematic re‐analysis of published evidence on ecological responses to altered flows

Summary Human-induced changes in river flow regimes are ubiquitous worldwide. Although numerous case studies have identified negative ecological impacts of changes in different aspects of flow regimes (e.g. magnitude, timing), there have been few attempts to systematically review this literature to derive general relationships regarding ecological responses to changes in flow regimes. Systematic literature reviews can inform science and management in ecologically complex systems not amenable to experimentation. However, such analysis of existing literature is often limited by inconsistent study design and data reporting. To attempt to overcome these difficulties, we used the recently developed Eco Evidence method and software to analyse 165 studies of ecological responses to changes in river flow regimes. Eco Evidence provides a rule set and standardised list of terms to assist reviewers to interpret consistently the results of disparate studies. The companion software assists with the synthesis of this information to reach transparent and repeatable conclusions regarding cause–effect hypotheses of ecological responses to environmental drivers. We compared our results to those of a recent, informal systematic review of the same studies, which is proving extremely influential. Stronger conclusions are reached when evidence is weighted, classified and combined according to the rules in Eco Evidence. Compared to the original review, we reached informative conclusions for a larger number of flow–response hypotheses, found that hypotheses for which the most evidence was available returned inconsistent results, addressed hypotheses at levels of conceptual resolution relevant to management and identified where insufficient evidence exists to reach a conclusion. Analyses conducted at several levels of conceptual resolution found strong support for many hypotheses regarding ecological impacts. We found a consistent sensitivity to changes in flow regime for both fish and riparian vegetation across a variety of performance metrics. While macroinvertebrate responses varied among performance metrics (e.g. abundance was negatively affected by increases or decreases in flows, diversity was only negatively affected by flow decreases, and assemblage structure was affected by neither), they were largely consistent within these metrics. We thus conclude that the Eco Evidence approach allowed us to extract more knowledge from the data set than was possible in the original review. Eco Evidence can improve synthesis of the burgeoning ecological literature and improve our general understanding in ecology. Amid widespread calls for ‘evidence-based’ environmental management, this powerful tool provides managers with a means of using research to help inform complex environmental decision-making.
LEAF ANATOMY OF CONOPHYTUM N. E. BR. (AIZOACEAE)

Abstract Leaf anatomy of Conophytum–a genus of 100 species of miniature xerophytic plants from the succulent Karoo in southern Africa–was examined using thin sections of plastic-embedded tissue and bright-field and polarized-light microscopy. Eighty-four species, from all recognized sections of the genus, were sectioned using material of known wild origin, with many species represented by multiple infraspecific taxa or populations. The broad scope of this investigation permits, for the first time, a meaningful study of the comparative anatomy of this large, morphologically diverse genus. The distribution of anatomical characters is described including: the pattern of deposition of calcium oxalate crystals in the epidermis, the presence and number of layers of hypodermis, and the presence and shape of tanniniferous idioblasts in the mesophyll. Typically xeromorphic characters like a hypodermis and epidermal crystal layers tend to be reduced or absent in species from sheltered niches, including soil-embedded, subterranean species with windowed leaves. Embedded species also frequently lack tannin cells, perhaps because their growth form reduces the need for chemical defenses against herbivores.
Inhibiting the NF-κB pathway enhances the antitumor effect of cabazitaxel by downregulating Bcl-2 in pancreatic cancer

Optimizing the currently available treatment options for pancreatic cancer (PC) is a priority. Cabazitaxel (CTX), a semisynthetic taxane, is mainly used for treating patients with PC who are resistant to paclitaxel (PTX) or docetaxel, due its poor affinity for P-glycoprotein. However, there are only a few studies demonstrating the effect of CTX on PC. The present study aimed to investigate the efficiency and underlying mechanism of CTX in PC treatment. Cell proliferation, colony formation assay and apoptosis analysis were achieved in the two human PC cell lines AsPC-1 and BxPC-3. Drug sensitivity test was performed in BxPC-3 tumor-bearing mice. The results demonstrated that CTX had a lower half maximal inhibitory concentration compared with PTX for the inhibition of cell proliferation, both in vivo and in vitro. Furthermore, the nuclear factor-κB (NF-κB) pathway was activated following cell treatment with CTX, and NF-κB p65 overexpression attenuated CTX cytotoxicity. In addition, the combined use of the specific NF-κB inhibitor caffeic acid phenethyl ester (CAPE) with CTX significantly enhanced CTX effect, both in vivo and in vitro. Similarly, the mRNA and protein expression of B-cell lymphoma-2 was decreased in AsPC-1 and BxPC-3 cells following treatment with CTX and CAPE, suggesting that NF-κB may serve a crucial role in CTX efficiency. In conclusion, results from our previous study indicated that CTX could potentially replace PTX in the treatment of PC, and the present study demonstrated that CTX combination with an NF-κB inhibitor may be considered as a potential therapeutic option for PC, which may improve the prognosis of patients with PC.
Preliminary Observations on Development of Pacific Bluefin Tuna Thunnus thynnus (Scombridae) Larvae Reared in the Laboratory, with Special Reference to the Digestive System

Pacific bluefin tuna larvae (Thunnus thynnus) were experimentally reared from 2-day-old yolk-sac larvae through 30-day-old early juveniles in June and July 1994. The larvae initially fed on rotifers on Day 3 and Artemia nauplii, fish eggs and larvae around Day 13, and thereafter were fed Artemia larvae and an artificial diet. The larvae had transformed to the juvenile stage after 30 days. The primitive digestive system differentiated on Day 3. The gastric gland and pyloric caeca first appeared on Day 11 and 14, respectively. The pharyngeal and jaw teeth became fully functional with gastric gland differentiation. The number of gastric glands and pyloric caeca and volume of the gastric blind sac increased markedly with development to the juvenile stage. Although the external morphological development of the tuna resembles the pattern of many other marine fish larvae, the basic digestive system developed at an earlier larval stage; this precocity may relate to the early appearance of piscivory and the high growth potential of tuna larvae.
The fine Structure of Amylopectin in Endosperm from Asian Cultivated Rice can be largely Classified into two Classes

1 The present investigations have been performed to characterize the structure of amylopectin in endosperm of rice plants cultivated in Asian countries, and to determine the relationship between the amylopectin structure and physicochemical properties of the starch. The results indicated that almost all of rice amylopectin was distinctly classified into L-type or S-type. The L-type amylopectin was diffrent from the S-type amylopectin in that the numbers of short α-1, 4-glucan chains of DP ≤ 10 were less than 20% of the total α-1, 4-glucan chains of DP ≤ 24 in a single cluster in the former and those were higher than 24% in the latter, while no significant difference between both types was found in the proportion of B2 and longer chains of DP ≥ 25. Strikingly, among the 129 rice varieties examined, only a single variety cv. Khauk Yoe belonging to the Tropical Japonica rice group had an intermediate amylopectin structure between L-type and S-type, called M-type amylopectin. Apparently, the proportion of chains with DP ≤10 to those with DP ≤ 24 in amylopectin molecules was negatively correlated with the onset temperature of gelatinization of the starch, whereas no such correlation was observed between the amylose content and the thermal properties of starch. All these results show that the varietal difference in amylopectin structure is predominantly due to difference in lengths of A chains of the cluster and plays a critical role in determining the physicochemical properties of starch in the rice endosperm.
Life history of Pygidiopsis crassus n. sp. (Trematoda, Digenea, Heterophyidae) in the neotropical region

The life cycle of Pygidiopsis crassus n. sp. was experimentally reproduced, starting from cercariae from naturally infected Littoridina parchappei collected from Lujan River and different ponds in Buenos Aires Province, Argentina. Metacercariae were found encysted in the body cavity of experimentally and naturally infected fishes Cnesterodon decemmaculatus and naturally infected Jenynsia lineata. Adults were obtained experimentally in chicks and mice. The natural host is unknown. The new species is compared with Pygidiopsis macrostomum Travassos 1928, from Rattus norvegicus and from Noctilio leporinus mastivus, differing in body and egg sizes, in the size relation of oral and ventral sucker and the shape of excretory vesicle.
Effects of Interferon-α on Cell Cycle Regulatory Proteins in Leukemic Cells

One prominent activity of Interferons (IFNs) is their ability to induce cell cycle arrest, and this effect has furthermore been proposed to be of major importance in mediating the clinical antitumor activity of IFNs. In several IFN sensitive established cell lines, a rapid upregulation of the cyclin dependent kinase inhibitor p21 occurs following IFN- α treatment, and is thought to play a major role as an effector for this phenomenon by triggering further events. The aim of this study was to investigate how these previous findings in established cells lines correlate with clinical material. We therefore, analyzed how IFN- α influences the cell cycle distribution, by analysis of cellular DNA content, and the level of various cell cycle regulatory proteins by Western blot analysis, in primary leukemic cells. In 5 of 10 examined acute myeloid leukemia samples and in 1 of 6 chronic lymphocytic leukemia sample a clear increase in p21 protein levels was detected following treatment with IFN- α, while p21 protein levels were unaffected by IFN treatment in any of the examined acute lymphoblastic leukemia samples. In our total material consisting of 21 patient samples all other cell cycle regulatory proteins studied (p27, Cyclin E, Cdk2), were largely unaffected by IFN treatment. These results confirm that IFN- α can act as a potent regulator of Cdk-inhibitor expression, and that the induction of p21 seems to be a primary event in IFN- α mediated cell cycle regulation.
Impact Wear of the Protective Cr3C2-Based HVOF-Sprayed Coatings

High velocity oxygen-fuel (HVOF) prepared CrC-based hardmetal coatings are generally known for their superior wear, corrosion, and oxidation resistance. These properties make this coating attractive for application in industry. However, under some loading conditions and in aggressive environments, the most commonly used NiCr matrix is not sufficient. The study is focused on the evaluation of dynamic impact wear of the HVOF-sprayed Cr3C2-25%NiCr and Cr3C2-50%NiCrMoNb coatings. Both coatings were tested by an impact tester with a wide range of impact loads. The Wohler-like dependence was determined for both coatings’ materials. It was shown that, due to the different microstructure and higher amount of tough matrix, the impact lifetime of the Cr3C2-50%NiCrMoNb coating was higher than the lifetime of the Cr3C2-25%NiCr coating. Differences in the behavior of the coatings were the most pronounced at high impact loads.
Prevalence of Ipsilateral Nonstenotic Carotid Plaques on Computed Tomography Angiography in Embolic Stroke of Undetermined Source

Supplemental Digital Content is available in the text. Background and Purpose— Embolic stroke of undetermined source (ESUS) constitutes a large proportion of acute ischemic stroke. It is crucial to identify possible stroke etiologies in this patient subgroup to individually tailor secondary stroke prevention strategies. This study aimed to assess the prevalence of carotid plaques causing <50% stenosis in ESUS patients on computed tomography angiography and the association of these plaques with ipsilateral strokes. Methods— Patients from INTERRSeCT—a multicenter prospective study of patients with acute ischemic stroke—were included in this study if their stroke etiology was not large artery atherosclerosis (>50% stenosis), and neck computed tomography angiography was obtained. Degree of stenosis (<30% versus 30%–50%), maximum plaque thickness, degree of plaque calcification (<50% versus ≥50%), plaque irregularity, ulceration, hypodensity, carotid web, and focal vessel outpouching were assessed for both carotid arteries on computed tomography angiography. Prevalence of carotid plaques with <50% stenosis (nonstenotic plaques), ipsilateral and contralateral to the stroke, in ESUS patients was determined and compared with non-ESUS patients. Features of these plaques with versus without ipsilateral stroke in ESUS patients were compared. Uni- and multivariable logistic regression was performed to determine associations between nonstenotic carotid plaque, plaque characteristics, and ipsilateral stroke in ESUS patients. Results— Four hundred forty-six patients were included in the study (median age, 73 years; 218 men), 138 of which were ESUS patients (median age, 70 years; 61 men). Nonstenotic carotid plaques (with <50% stenosis) were present in 54 of 138 (39.1%) ESUS patients. Twelve (8.7%) patients had bilateral carotid plaques. Forty (60.6%) of these plaques were ipsilateral and 26 (39.4%) contralateral to the side of the stroke (P=0.004). Nonstenotic carotid plaques were significantly associated with ipsilateral strokes (adjusted odds ratio, 1.83 [95% CI, 1.05–3.18]). Conclusions— In patients with ESUS, nonstenotic carotid plaques were significantly more common on the side of the ischemic stroke, suggesting that these plaques could be a potential stroke etiology in patients in whom the ischemic stroke is classified currently as ESUS.
Frequency of Resistance to Benzimidazoles of Haemonchus contortus Helminths from Dairy Sheep, Goats, Cattle and Buffaloes in Greece

The study investigated the presence of resistance to benzimidazoles in Haemonchus contortus helminths from ruminant species in Greece through the detection of the Phe/Tyr polymorphism in the amino acid at position 200 of the β-tubulin protein. In total, 288 adult female H. contortus helminths collected from the abomasum of various ruminant animals in Greece were tested. Of these, 96 were collected from sheep, 96 from goats, 48 from cattle, and 48 from buffaloes. The frequencies of the homozygous and heterozygous resistant genotypes at the position 200 of the β-tubulin gene of helminths recovered from sheep were 96.9% and 3.1%, respectively. The frequencies of the homozygous and heterozygous resistant genotypes, respectively, were 100.0% and 0.0% in helminths from goats, 25.0% and 75.0% in helminths from cattle and 8.3% and 91.7% in helminths from buffaloes. In all parasitic populations, no homozygous susceptible genotypes were detected. The present study highlighted, for the first time, the emergence of benzimidazole-resistant H. contortus in goats, cattle, and buffaloes in Greece, using an allele-specific PCR. It is postulated that benzimidazole-resistant alleles were transferred from sheep or goats to cattle and buffaloes at the commonly grazing pastures in Greece.
Properties of Phenolic Composition and Biological Activity of Propolis from Turkey

Propolis has highly biologically active natural substances. Propolis is rich in phenolic compounds, and is becoming increasingly popular because of its components' potential role in contributing to human health. Its composition is variable and depends on several factors. In this study, some individual phenolic compounds were analyzed and investigated in vitro biological activities of ten different Turkish propolis samples. Seventeen different phenolic constituents were measured by reverse phase-high performance liquid chromatography. Total phenolic compounds and ferric reducing antioxidant power were used as antioxidant capacity determinants. The antimicrobial activity was studied by agar diffusion method using six bacteria and two yeasts. All propolis showed strong antioxidant and antimicrobial activity and contained large amounts of antioxidant compounds. Quercetin, benzoic acid, caffeic acid, ferulic acid, and coumaric acid were detected in all propolis samples in high amounts, while vanillic acid, chlorogenic acid, epicathecin, rutin, syringic acid, and o-coumaric acid were found in very small quantities and cathecin was not found in any of them. The methanolic extracts were active against all bacteria and yeasts. They were especially effective against Pseudomonas aeruginosa ATCC®27853. The propolis extracts proved to be a good source of antioxidants and antimicrobial agents that might serve to protect health and fight against several diseases.
Development of a single-stranded DNA-binding protein fluorescent fusion toolbox

Abstract Bacterial single-stranded DNA-binding proteins (SSBs) bind single-stranded DNA and help to recruit heterologous proteins to their sites of action. SSBs perform these essential functions through a modular structural architecture: the N-terminal domain comprises a DNA binding/tetramerization element whereas the C-terminus forms an intrinsically disordered linker (IDL) capped by a protein-interacting SSB-Ct motif. Here we examine the activities of SSB-IDL fusion proteins in which fluorescent domains are inserted within the IDL of Escherichia coli SSB. The SSB-IDL fusions maintain DNA and protein binding activities in vitro, although cooperative DNA binding is impaired. In contrast, an SSB variant with a fluorescent protein attached directly to the C-terminus that is similar to fusions used in previous studies displayed dysfunctional protein interaction activity. The SSB-IDL fusions are readily visualized in single-molecule DNA replication reactions. Escherichia coli strains in which wildtype SSB is replaced by SSB-IDL fusions are viable and display normal growth rates and fitness. The SSB-IDL fusions form detectible SSB foci in cells with frequencies mirroring previously examined fluorescent DNA replication fusion proteins. Cells expressing SSB-IDL fusions are sensitized to some DNA damaging agents. The results highlight the utility of SSB-IDL fusions for biochemical and cellular studies of genome maintenance reactions.
Biology and fertility life table of the greenbug, Schizaphis graminum (Hemiptera: Aphididae) on the resistant winter wheat cultivar (Pishgam) in Iran

The greenbug, Schizaphis graminum (Rondani) (Hemiptera: Aphididae) has been known as a major pest of small grains, particularly wheat, worldwide. In this study, the effect of new wheat cultivar (Pishgam) for cold regions on biological characteristics of greenbug was investigated in a greenhouse at 25 ± 2 °C, 55 ± 10% relative humidity and a photoperiod of 16:8 h (L:D). The raw data were analysed based on the age-stage, two-sex life table. The intrinsic rate of increase (r), the finite rate of increase (λ), the net reproduction rate (R0) and the mean generation time (T) of greenbug were 0.313 ± 0.0019, 1.36 ± 0.0027 females/female/day, 83.33 ± 0.331 females/female and 14.11 ± 0.09 days, respectively. The life expectancy of a nymph is 43.57 days. The maximum reproductive value of females is on the 16th day which coincides with the total pre-reproduction period counted from birth. Hence, the present results may provide helpful information for comprehensive IPM programme of greenbug on this variety in cold regions of Iran. Result revealed that nymphal survival rate of the aphid was 100% on studied cultivar like that on sensitive host plant cultivar.