Miracle-dz/UniFAR-FTUs huggingface dataset:
Flow restoration and the impacts of multiple stressors on fish communities in regulated rivers

River regulation for hydropower is undertaken worldwide, causing profound alterations to hydrological regimes and running water habitats. Regulated catchments are often subjected to additional stressors, arising inter alia from agriculture, forestry and industry, which are likely to interact with impacts of river regulation on fish and other biota. Such interactions are poorly understood, hindering planning of effective mitigation and restoration. We investigated fish responses to increased discharge (as a restoration measure) in regulated rivers in Sweden. We compiled electrofishing data from river channels downstream of hydropower dams, each of which either has or lacks a mandated minimum discharge corresponding to c. 5% of pre‐regulation discharge. We further analysed interactions between flow restoration and co‐occurring local and regional stressors. River channels without a mandated minimum discharge were characterized by a low diversity of fish species with traits favouring persistence under unpredictable environmental conditions, including omnivory, short life cycles and small size. Additional stressors further reduced diversity and increased dominance by broad‐niched, opportunistic species. Both the presence and magnitude of a mandated minimum discharge were positively related to fish diversity and density, and the relative density of three economically and recreationally valuable species. However, the size of these relationships frequently varied with the presence of additional stressors. Increasing levels of hydrological degradation and reduced connectivity at the catchment scale reduced positive flow–ecology relationships and hindered the restoration of fish communities towards reference conditions. However, application of a mandated minimum discharge also assisted in mitigating impacts of some co‐occurring stressors, especially reduced riparian integrity. Synthesis and applications. Additional stressors can strongly influence the outcomes of flow restoration for fish community diversity and composition. Our approach combining fish species and trait data from multiple flow restoration projects with information on additional stressors yielded valuable insights into factors affecting flow restoration success, useful for (a) identifying the systems most likely to benefit from mandated minimum flows, (b) modelling influences of multiple stressors on flow–ecology relationships, (c) prioritizing additional measures to manage co‐occurring stressors and enhance outcomes from flow restoration.
Gene therapy and retinitis pigmentosa: advances and future challenges

It may be possible, one day, to use gene therapy to treat diseases whose genetic defects have been discerned. Because many genes responsible for inherited eye disorders within the retina have been identified, diseases of the eye are prime candidates for this form of therapy. The eye also has the advantage of being highly accessible with altered immunological properties, important considerations for easy delivery of virus and avoidance of systemic immune responses. Currently, adenovirus, adeno‐associated virus and lentivirus have been used to successfully transfer genetic material to retinal pigment epithelium and photoreceptor cells. By harnessing therapeutic genes to these viruses, researchers have been able to demonstrate rescue in rodent models of retinitis pigmentosa, providing evidence that this form of therapy can be effective in delaying photoreceptor cell death. Future challenges include confirming therapeutic effects in animal models with eyes more anatomically similar to those of humans and demonstrating long‐term rescue with minimal toxicity. BioEssays 23:662–668, 2001. © 2001 John Wiley & Sons, Inc.
Localization of the complex spectrum: the S transform

The S transform, which is introduced in the present correspondence, is an extension of the ideas of the continuous wavelet transform (CWT) and is based on a moving and scalable localizing Gaussian window. It is shown to have some desirable characteristics that are absent in the continuous wavelet transform. The S transform is unique in that it provides frequency-dependent resolution while maintaining a direct relationship with the Fourier spectrum. These advantages of the S transform are due to the fact that the modulating sinusoids are fixed with respect to the time axis, whereas the localizing scalable Gaussian window dilates and translates.
Measuring outcome in posttraumatic stress disorder.

This article summarizes the features of posttraumatic stress disorder (PTSD) that may affect treatment outcome and discusses the areas in which treatment outcome can be productively evaluated. PTSD is a complex psychiatric condition that tends to run a chronic course. Measurement of treatment outcome in PTSD is confounded by multiple factors, including a high prevalence of comorbid disorders, reactivation of the syndrome by ongoing environmental stressors, spontaneous recovery of the early disorder, and a fluctuating course of the chronic disorder. Four principal domains of treatment outcome may be evaluated in PTSD: core symptom severity, comorbid conditions (particularly depression), adverse practices (e.g., violence or alcohol consumption), and social/vocational disability. To gain an accurate assessment of these domains, a comprehensive assessment battery is needed. The relevant instruments and their yield in studies of PTSD are reviewed.
Paromomycin binding induces a local conformational change in the A-site of 16 S rRNA.

Aminoglycoside antibiotics that bind to ribosomal RNA in the aminoacyl-tRNA site (A-site) cause misreading of the genetic code and inhibit translocation. An A-site RNA oligonucleotide specifically binds to aminoglycoside antibiotics and the structure of the RNA-paromomycin complex was previously determined by nuclear magnetic resonance (NMR) spectroscopy. Here, the A-site RNA structure in its free form has been determined using heteronuclear NMR and compared to the structure of the paromomycin-RNA complex. As in the complex with paromomycin, the asymmetric internal loop is closed by a Watson-Crick base-pair (C1407.G1494) and by two non-canonical base-pairs (U1406.U1495, A1408.A1493). A1492 stacks below A1493 and is intercalated between the upper and lower stems. The comparison of the free and bound conformations of the RNA shows that two universally conserved residues of the A site of 16 S rRNA, A1492 and A1493, are displaced towards the minor groove of the RNA helix in presence of antibiotic. These changes in the RNA conformation place the N1 positions of A1492 and A1493 on the minor groove side of the A-site RNA and suggest a mechanism of action of aminoglycosides on translation.
Mycobacterium smegmatis RNA polymerase: DNA supercoiling, action of rifampicin and mechanism of rifampicin resistance

We have isolated RNA polymerase from Mycobacterium smegmatis and established conditions for specific transcription initiation in vitro. The M. smegmatis enzyme has a strong dependence on supercoiling of the DNA substrate for transcription from mycobacterial promoters. We also show that RNA polymerase is the target for rifampicin, and that this antibiotic specifically inhibits the transition from synthesis of short oligoribonucleotides to full‐length transcripts. RNA polymerase isolated from a rifampicin‐resistant mutant of M. smegmatis is less sensitive to rifampicin in vitro, confirming that one mechanism of rifampicin resistance in mycobacteria is through alteration of RNA polymerase. This in vitro transcription system provides a simple method for the characterization of gene expression in mycobacteria including the pathogens Mycobacterium tuberculosis, Mycobacterium avium and Mycobacterium leprae. It also provides a system for evaluating potential anti‐mycobacterial drugs.
Airborne measurement of inorganic ionic components of fine aerosol particles using the particle‐into‐liquid sampler coupled to ion chromatography technique during ACE‐Asia and TRACE‐P

[1] Eight inorganic ions in fine aerosol particles (Dp 1 ppbv only in the top 1% sample population. During TRACE-P, NH4+ dominated, followed by SO42−, Cl−, Na+, NO3−, Ca2+, and K+, in decreasing order of importance. In addition to a sea-salt origin, Cl− showed a source in urban emissions possibly related to biofuel combustion. Both sea salt and dust contributed to Mg2+. In both experiments, NH4+, SO42−, NO3−, and CO were strongly correlated, indicating that combustion was the dominant source of these species and that NH3 and other alkaline materials were in sufficient supply to neutralize H2SO4. The [NH4+] to ([NO3−] + 2[SO42−]) ratio was ∼0.70 in the two campaigns, with deviations found only in volcano plumes, whereby SO42− was found to correlate with SO2. Charge balance of the ions showed both positive and negative deviations whose magnitudes, ∼30%, provide estimates of the lower limits of unmeasured ions. Elevated NO3− and Ca2+ coexist mainly under polluted conditions, suggesting the importance of sequestering HNO3 by mineral dust.
Sox2 and Pax6 maintain the proliferative and developmental potential of gliogenic neural stem cells In vitro

Radial‐glia‐like neural stem (NS) cells may be derived from neural tissues or via differentiation of pluripotent embryonic stem (ES) cells. However, the mechanisms controlling NS cell propagation and differentiation are not yet fully understood. Here we investigated the roles of Sox2 and Pax6, transcription factors widely expressed in central nervous system (CNS) progenitors, in mouse NS cells. Conditional deletion of either Sox2 or Pax6 in forebrain‐derived NS cells reduced their clonogenicity in a gene dosage‐dependent manner. Cells heterozygous for either gene displayed moderate proliferative defects, which may relate to human pathologies attributed to SOX2 or PAX6 deficiencies. In the complete absence of Sox2, cells exited the cell cycle with concomitant downregulation of neural progenitor markers Nestin and Blbp. This occurred despite expression of the close relative Sox3. Ablation of Pax6 also caused major proliferative defects. However, a subpopulation of cells was able to expand continuously without Pax6. These Pax6‐null cells retained progenitor markers but had altered morphology. They exhibited compromised differentiation into astrocytes and oligodendrocytes, highlighting that the role of Pax6 extends beyond neurogenic competence. Overall these findings indicate that Sox2 and Pax6 are both critical for self‐renewal of differentiation‐competent radial glia‐like NS cells. © 2011 Wiley‐Liss, Inc.
The Arabidopsis thaliana CONSTANS-LIKE 4 (COL4) – A Modulator of Flowering Time

Appropriate control of flowering time is crucial for crop yield and the reproductive success of plants. Flowering can be induced by a number of molecular pathways that respond to internal and external signals. In Arabidopsis, expression of the key florigenic signal FLOWERING LOCUS T (FT) is positively regulated by CONSTANS (CO) a BBX protein sharing high sequence similarity with 16 CO-like proteins. Within this study, we investigated the role of the Arabidopsis CONSTANS-LIKE 4 (COL4), whose role in flowering control was unknown. We demonstrate that, unlike CO, COL4 is a flowering repressor in long days (LD) and short days (SD) and acts on the expression of FT and FT-like genes as well as on SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1). Reduction of COL4 expression level leads to an increase of FT and APETALA 1 (AP1) expression and to accelerated flowering, while the increase of COL4 expression causes a flowering delay. Further, the observed co-localization of COL4 protein and CO in nuclear speckles supports the idea that the two act as an antagonistic pair of transcription factors. This interaction may serve the fine-tuning of flowering time control and other light dependent plant developmental processes.
Treatment of fractures of the distal femoral – overviews of osteosynthesis funds

Distal femoral fractures thigh up from 4 to 9% of all fractures of the femur. There is a direct relationship between the mechanism of receipt of the lesion and the age, sex and the type of fracture. Caused mainly by high-traumatic effects and lead to a high degree of disability. For these reasons, injuries in this anatomical area are of great social importance. The goal of the distal femur fractures treatment is to recover patients preoperative status for the shortest possible period. This may be achieved by open reposition and internal fixation. Recent years are characterized by significant progress in the treatment of this type of fracture. This is due to the rapid development of new and sound biomechanical implants: 95 ° Angled blade plates (ABP), condylar buttress plates (CBP), dynamic condylar screw (DCS), retrograde intramedullary nails (two locking or a locking screw + spiral blade), LISS-plates. The discussion in the treatment of these fractures is concentrated in the choice of means of internal fixation by which to achieve the greater stability of the individual type of fracture.
Prognostic Value of Fibroblast Growth Factor Receptor 1 Gene Locus Amplification in Resected Lung Squamous Cell Carcinoma

Introduction: Fibroblast growth factor receptor 1 (FGFR1) gene amplification was recently reported as a recurrent abnormality in 10% to 20% of primary lung squamous cell carcinomas (SqCCs), and has attracted significant interest as a potential therapeutic target. Limited data are available for its prognostic impact in early-stage SqCC. Methods: Tissue microarrays containing 135 primary lung SqCCs and 58 matching lymph node metastases were tested by interphase fluorescence in situ hybridization for DNA copy number (CN) abnormalities at the 8p12 region including FGFR1. Results: FGFR1amplification was found in 18.2% (22 of 121 evaluable) of primary SqCC, using a definition of average copies of FGFR1 per cell of 5.0 or more. Concordance rate between primaries and matching lymph node metastases was 97.7% (43 of 44; 7 amplified and 37 nonamplified), with the only discordant case showing CN at approximately the dichotomous cutoff. Similarly, concordance between two separate lymph node metastases in each of 10 patients was 100% (1 amplified and 9 nonamplified). Using various CN cutoffs, we found no statistically significant association between FGFR1 CN abnormalities and patient age, sex, tumor grade, stage, smoking status, disease-free survival, cause-specific survival, or overall survival. Conclusion: FGFR1 amplification is not prognostic in resected lung squamous cell carcinoma patients.
Usnic acid and its versatility as MALDI matrix.

Lichens are resilient organisms capable of surviving under extreme conditions such as extended periods of desiccation and severe UV radiation. Being symbionts of fungi with algae or cyanobacteria, they exhibit a unique profile of secondary metabolites including depsides and depsidones, which aremainly studied for their biological activities. However from a chemical perspective these phenol derivatives also show close structural similarities to matrices commonly used in matrix assisted laser desorption ionization (MALDI). With this in mind the present study evaluated four relatively easily accessible lichenmetabolites for their potential application as MALDI matrices. These compounds were: 2,6-diacetyl-7,9-dihydroxy-8,9bdimethyl-1,3(2H,9bH)-dibenzo-furandione, also known as ( ) usnic acid (1a), its stereoisomer (+) usnic acid (1b), 2,4-dihydroxy-3-[(2hydroxy-4-methoxy-6-propylbenzoyl)oxy]-6-propyl-benzoic acid methyl ester, also known as m-scrobiculin (2), and 4,6-diformyl8-hydroxy-3-methoxy-1,9-dimethyl-11-oxo-11H-dibenzo[b,e][1,4] dioxepin-7-carboxylic acid (3) (Fig. 1). Low and medium mass range analytes such as horse myoglobin, cytochrome C, porcine insuline, gramidicin (A–D), substance P, angiotensin II, yohimbine as well as a multicomponent peptide mixture were used to evaluate the ionization properties of 1a-3. The experiments were performed in the positive and the negative ionization mode. Eventually, a direct comparison of 1a with commercial matrices such as α-cyano-4-hydroxycinnamic acid (4) and 2,5dihydroxybenzoic acid (5) was conducted.
Printing in Organ Transplantation

An insufficient supply of organs for transplant is an ever present obstacle for transplant medicine. A long term resolution of these problems is being sought by developing ways to engineer live organs from a person’s own cells. Previous tissue manufacturing approaches involved seeding either adult or stem cells onto various 3D scaffolds, with subsequent cell proliferation and differentiation into spatially-arranged functional tissue. However, the approach has not been successful as organs are very complicated. Advances in our understanding of an organ’s tissue components and progress in 3D printing technology have allowed a new era of bioprinting to unfold. Bioprinting is described as a 3D printing system that provides precise accumulation and arrangement of living cells, extracellular matrix elements, biochemical components, proteins, and bio-substances on solid or gel reservoirs that can closely mimic the living organ which is being artificially constructed [1-4]. Substantial achievements in understanding the intricate structure of organs have led researchers to conclude that artificial organ construction demands highly accurate placement of these components including complex vascular integration [5]. Recent advances in the development of 3D printers utilizing laser-based, inkjet-based and extrusion systems have facilitated the development of techniques that allow the construction of these intricate organ structures with precise arrangement of matrix, vasculature and cells [6]. Bio-printing is providing a greater ability in tissue engineering and researchers are hoping to be able to manufacture de novo living organs for transplant in the near future to alleviate the chronic shortage of Hanyang Med Rev 2014;34:158-164 http://dx.doi. org/10.7599/hmr.2014. 34.4. 158
Variation in Deoxynivalenol, 15-Acetyldeoxynivalenol, 3-Acetyldeoxynivalenol, and Zearalenone Production by Fusarium graminearum Isolates

Of 88 isolates of Fusarium graminearum collected from soil or cereals in the United States, 49 produced 15-acetyldeoxynivalenol (15-ADON) as the major isomer; one produced 3-acetyldeoxynivalenol (3-ADON). A total of 26 isolates collected from cereals or soil in Australia, New Zealand, Norway, China, and Poland were used for comparison. Of these, 15 produced 3-ADON as the major isomer and 2 produced 15-ADON.
Depolarization of normal and preganglionically denervated superior cervical ganglia by stimulant drugs.

Evidence has recently been obtained to suggest that degenerative section of the preganglionic cervical sympathetic nerve trunk does not increase, but rather reduces, the sensitivity of the cat superior cervical ganglion to carbachol and other cholinesterase-resistant stimulant drugs Koelle, In this study the postganglionic nerve discharges following close-arterial injection of stimulant drugs were recorded in vivo.
Effects of vaccination against Yersinia ruckeri on oxidative stress biomarkers and liver and heart biochemistry in rainbow trout (Oncorhynchus mykiss)

Abstract To determine the effects of vaccination against Yersinia ruckeri on the health condition of rainbow trout, Oncorhynchus mykiss (Walbaum) in general, and oxidative stress biomarkers and metabolic parameters specifically, as well as to identify mechanisms that underpin the susceptibility of fish to vaccination, we compared the liver and heart function, and the oxidative mechanism underlying those effects, by detecting relevant lipid peroxidation and protein oxidation biomarkers, as well as aerobic-anaerobic metabolism in trout immunized against Y. ruckeri at 30 days post-vaccination and in healthy individuals. In our study, hepatic aminotransferase activities were positively associated with the oxidative stress biomarkers in the trout vaccinated against Y. ruckeri. Moreover, similar associations were observed in the cardiac tissue of the immunized trout. Decreased aldehydic and ketonic derivatives of oxidatively modified proteins and the reduction of aminotransferase and lactate dehydrogenase activities were sensitive to the vaccination of trout against Y. ruckeri and may potentially be used as biomarkers in evaluating vaccine effects in the liver of rainbow trout. Understanding the role of biochemical changes in the tissues of vaccinated trout has important implications for understanding of the complex physiological changes that occur in immunization, and also for improving aquaculture practices to maximize tissue growth and the health of vaccinated trout.
Impact of variation in limb shape on sub-bandage interface pressure

Background Sub-bandage interface pressure generated by medical compression bandages (MCB) and hosiery changes in mobile patients as they move due to the change in the limb size. However, the amount of variation in the interface pressure is dependent on the stiffness of the compression material. Researchers have proposed several indices to describe this change in interface pressure, including the static stiffness index (SSI) and the dynamic stiffness index (DSI). These indices can also be used to classify compression products. Objectives To explore the different proposed indices to describe the stiffness of a compression material and compare it to the engineering stress-strain modulus which is used for the same purpose; To estimate theoretically the change in the interface pressure which is caused by the change in the limb shape as a consequence of calf muscle activity and the associated transient variation in limb dimensions. Method Use Chord modulus to classify compression material; Use thin and thick cylinder wall theory to estimate the variation in the interface pressure due to changes in the limb shape secondary to muscle contraction; Use tensile test devices to obtain the Chord modulus for two different MCB at two different dynamic ranges. Results Chord modulus (E) describes the change in tension in a dynamic situation, and this is labelled as stiffness in the bandaging literature; Chord modulus, with the help of a mathematical model that was developed based on thick wall cylinder theory, can be used to predict the change in sub-bandage interface pressure caused by the change in limb shape secondary to calf muscle activity; Chord modulus can be used to classify bandages and describe how they will behave when they are applied to a leg. Conclusion The dynamic pressure can be predicted using a simple mathematical model using Chord modulus, which can be calculated in vitro using standard tensile testing equipment. In addition, Chord modulus can be used to classify compression bandages and hosiery.
Epidemiological research at the American Cancer Society.

When the ACS[2][1] founded its intramural program of epidemiological research in 1946, lung cancer death rates in men had increased approximately 5-fold since 1930, the first year for which mortality statistics encompassed most of the United States ,[(1)][2] . Death rates from what had been the two