Miracle-dz/UniFAR-FTUs huggingface dataset:
Using ecological production functions to link ecological processes to ecosystem services

Ecological production functions (EPFs) link ecosystems, stressors, and management actions to ecosystem services (ES) production. Although EPFs are acknowledged as being essential to improve environmental management, their use in ecological risk assessment has received relatively little attention. Ecological production functions may be defined as usable expressions (i.e., models) of the processes by which ecosystems produce ES, often including external influences on those processes. We identify key attributes of EPFs and discuss both actual and idealized examples of their use to inform decision making. Whenever possible, EPFs should estimate final, rather than intermediate, ES. Although various types of EPFs have been developed, we suggest that EPFs are more useful for decision making if they quantify ES outcomes, respond to ecosystem condition, respond to stressor levels or management scenarios, reflect ecological complexity, rely on data with broad coverage, have performed well previously, are practical to use, and are open and transparent. In an example using pesticides, we illustrate how EPFs with these attributes could enable the inclusion of ES in ecological risk assessment. The biggest challenges to ES inclusion are limited data sets that are easily adapted for use in modeling EPFs and generally poor understanding of linkages among ecological components and the processes that ultimately deliver the ES. We conclude by advocating for the incorporation into EPFs of added ecological complexity and greater ability to represent the trade‐offs among ES. Integr Environ Assess Manag 2017;13:52–61. © 2016 SETAC.
Quantitative X‐ray projection microscopy: phase‐contrast and multi‐spectral imaging

We outline a new approach to X‐ray projection microscopy in a scanning electron microscope (SEM), which exploits phase contrast to boost the quality and information content of images. These developments have been made possible by the combination of a high‐brightness field‐emission gun (FEG)‐based SEM, direct detection CCD technology and new phase retrieval algorithms. Using this approach we have been able to obtain spatial resolution of < 0.2 µm and have demonstrated novel features such as: (i) phase‐contrast enhanced visibility of high spatial frequency image features (e.g. edges and boundaries) over a wide energy range; (ii) energy‐resolved imaging to simultaneously produce multiple quasi‐monochromatic images using broad‐band polychromatic illumination; (iii) easy implementation of microtomography; (iv) rapid and robust phase/amplitude‐retrieval algorithms to enable new real‐time and quantitative modes of microscopic imaging. These algorithms can also be applied successfully to recover object–plane information from intermediate‐field images, unlocking the potentially greater contrast and resolution of the intermediate‐field regime. Widespread applications are envisaged for fields such as materials science, biological and biomedical research and microelectronics device inspection. Some illustrative examples are presented. The quantitative methods described here are also very relevant to projection microscopy using other sources of radiation, such as visible light and electrons.
Can Anaerobic Performance Be Improved by Remote Ischemic Preconditioning?

Abstract Lalonde, F, and Curnier, DY. Can anaerobic performance be improved by remote ischemic preconditioning? J Strength Cond Res 29(1): 80–85, 2015—Remote ischemic preconditioning (RIPC) provides a substantial benefit for heart protection during surgery. Recent literature on RIPC reveals the potential to benefit the enhancement of sports performance as well. The aim of this study was to investigate the effect of RIPC on anaerobic performance. Seventeen healthy participants who practice regular physical activity participated in the project (9 women and 8 men, mean age 28 ± 8 years). The participants were randomly assigned to an RIPC intervention (four 5-minute cycles of ischemia reperfusion, followed by 5 minutes using a pressure cuff) or a SHAM intervention in a crossover design. After the intervention, the participants were tested for alactic anaerobic performance (6 seconds of effort) followed by a Wingate test (lactic system) on an electromagnetic cycle ergometer. The following parameters were evaluated: average power, peak power, the scale of perceived exertion, fatigue index (in watt per second), peak power (in Watt), time to reach peak power (in seconds), minimum power (in Watt), the average power-to-weight ratio (in watt per kilogram), and the maximum power-to-weight ratio (in watt per kilogram). The peak power for the Wingate test is 794 W for RIPC and 777 W for the control group (p = 0.208). The average power is 529 W (RIPC) vs. 520 W for controls (p = 0.079). Perceived effort for RIPC is 9/10 on the Borg scale vs. 10/10 for the control group (p = 0.123). Remote ischemic preconditioning does not offer any significant benefits for anaerobic performance.
Predicting Co-Complexed Protein Pairs Based on Communication Model Using Diverse Biological Data

Protein-protein interactions play key role in many fundamental biological processes, and comprehensively identifying them represents a crucial step towards systematically defining their cellular roles. Machine learning techniques have been employed to predict protein-protein interactions. One of such approaches is Naive Bayes approach which assumes conditional independence between features. And such problems as suffering from the missing value problems or being prohibitively time-consuming prevent them from being applied to predict PPI as readily as NB. In this work, we frame predicting PPI as a communication problem, and we train a classifier based on channel model (CBCM) to discriminate between pairs of proteins that are co-complexed and pairs that are not. We theoretically demonstrate that NB can be unified into CBCM in certain condition and also experimentally validate that CBCM is an effective approach for predicting co-complexed protein pairs from integrating diverse biological data. Our study suggests that PPI prediction problem can be effectively solved from the point view of communication problem.
Mutations of temperature sensitivity in R plasmid pSC101

Temperature-sensitive (Ts) mutant plasmids isolated from tetracycline resistance R plasmid pSC101 were investigated for their segregation kinetics and deoxyribonucleic acid (DNA) replication. The results fit well with the hypothesis that multiple copies of a plasmid are distributed to daughter cells in a random fashion and are thus diluted out when a new round of plasmid DNA replication is blocked. When cells harboring type I mutant plasmids were grown at 43 degrees C in the absence of tetracycline, antibiotic-sensitive cells were segregated after a certain lag time. This lag most likely corresponds to a dilution of plasmids existing prior to the temperature shift. The synthesis of plasmid DNA in cells harboring type I mutant plasmids was almost completely blocked at 43 degrees C. It seems that these plasmids have mutations in the gene(s) necessary for plasmid DNA replication. Cells haboring a type II mutant plasmid exhibited neither segregation due to antibiotic sensitivity nor inhibition of plasmid DNA replication throughout cultivation at high temperature. It is likely that the type II mutant plasmid has a temperature-sensitive mutation in the tetracycline resistance gene. Antibiotic-sensitive cells haboring type III mutant plasmids appeared at high frequency after a certain lag time, and the plasmid DNA synthesis was partially suppressed at the nonpermissive temperature. They exhibited also a pleiotrophic phenotype, such as an increase of drug resistance level at 30 degrees C and a decrease in the number of plasmid genomes in a cell.
MitoPark mice mirror the slow progression of key symptoms and L‐DOPA response in Parkinson's disease

The MitoPark mouse, in which the mitochondrial transcription factor Tfam is selectively removed in midbrain dopamine (DA) neurons, is a genetic model for Parkinson's disease (PD) that replicates the slow and progressive development of key symptoms. To further validate this model, we have extended both behavioral and biochemical analyses in these animals. We found that vertical movements decline earlier and faster than horizontal movements, possibly modeling the early occurrence of axial, postural instability in PD. L‐DOPA induces different locomotor responses depending on the age: in young MitoPark mice the L‐DOPA‐induced motor activation is small; middle‐aged MitoPark mice respond in a dose‐dependent manner to L‐DOPA, whereas aged MitoPark mice display a double‐peaked locomotor response to a high dose of L‐DOPA that includes an intermittent period of very low motor activity, similar to the ‘on–off’ phenomenon in PD. To correlate behavior with biochemical data, we analyzed monoamine levels in three different brain areas that are highly innervated by the DA system: striatum, anterior cortex and olfactory bulb. DA levels declined earlier and faster in striatum than in cortex; only at the latest time‐point analyzed, DA levels were found to be significantly lower than control levels in the olfactory bulb. Interestingly, the ratio between homovanillic acid (HVA) and DA differed between regions over time. In striatum and olfactory bulb, the ratio increased steeply indicating increased DA turnover. In contrast, the ratio decreased over time in cortex, revealing important differences between DA cells in substantia nigra and the ventral tegmental area.
Direct Estimating Price of a Defaultable Zero-Coupon Bond Using Conception of Continuous Coupon Bond

In this paper, using a conception of continuous coupon bond with continuous accrual of coupons on simple fixed rate for pricing a risky zero-coupon bond is considered. It is shown that only employing this conception allows obtaining explicit equation for price of risky zero-coupon bond from fixed coupon bond prices without any assumption about default process and providing continuous monitoring default events despite periodicity of bond cash flows that improves estimation of credit risk. To apply the conception, it is proposed a simple condition for inversion of discrete bond into continuous coupon one. It is shown that this inversion is possible only for the following recovery assumption: a recovery rate is a part of the present value of remaining cash flows that will not be paid due to default but not for the fractional recovery of par assumption. Examples of calculating the implied survival probabilities and the credit spreads for Ukrainian Eurobonds are given.
BRPF 3-HBO 1 regulates replication origin activation and histone H 3 K 14 acetylation

Thank you for submitting your manuscript on BRPF3-HBO1 roles in replication origin firing for consideration by The EMBO Journal. It has now been assessed by three expert referees, whose reports you will find copied below. Although all three reviewers in principle consider the new postlicensing HBO1 role involving H3 targeting by a distinct cofactor potentially interesting, they currently remain unconvinced that all of the main conclusions are fully supported by sufficiently compelling evidence. As you will see, especially referees 1 and 3 raise a number of specific points that in their view require additional experimentation. The overriding key concern, stated explicitly by referees 1 and 2, is the the need to demonstrate a direct and local effect of the identified BRPF3HBO1-H3K14Ac-Cdc45 axis at selected origins. In the absence of such demonstration, I am afraid it would seem premature for us to commit to eventual future acceptance and publication in The EMBO Journal at this stage.
Nuclear gene silencing directs reception of long-distance mRNA silencing in Arabidopsis

In plants, silencing of mRNA can be transmitted from cell to cell and also over longer distances from roots to shoots. To investigate the long-distance mechanism, WT and mutant shoots were grafted onto roots silenced for an mRNA. We show that three genes involved in a chromatin silencing pathway, NRPD1a encoding RNA polymerase IVa, RNA-dependent RNA polymerase 2 (RDR2), and DICER-like 3 (DCL3), are required for reception of long-distance mRNA silencing in the shoot. A mutant representing a fourth gene in the pathway, argonaute4 (ago4), was also partially compromised in the reception of silencing. This pathway produces 24-nt siRNAs and resulted in decapped RNA, a known substrate for amplification of dsRNA by RDR6. Activation of silencing in grafted shoots depended on RDR6, but no 24-nt siRNAs were detected in mutant rdr6 shoots, indicating that RDR6 also plays a role in initial signal perception. After amplification of decapped transcripts, DCL4 and DCL2 act hierarchically as they do in antiviral resistance to produce 21- and 22-nt siRNAs, respectively, and these guide mRNA degradation. Several dcl genotypes were also tested for their capacity to transmit the mobile silencing signal from the rootstock. dcl1–8 and a dcl2 dcl3 dcl4 triple mutant are compromised in micro-RNA and siRNA biogenesis, respectively, but were unaffected in signal transmission.
Online Tool Wear Monitoring Via Hidden Semi-Markov Model With Dependent Durations

The tool wear monitoring (TWM) system that could estimate tool wear conditions and predict remaining useful life (RUL) is important to meet the high precision requirement and improve productivity in automated machining. Due to its good properties in representing nonstationary and complex physical process, hidden semi-Markov Model (HSMM) is adapted to model the progressive tool wear in this paper. In order to describe the time-variant transition probability of tool wear states and the state duration dependency, the HSMM is improved by learning the duration parameters and RUL distribution database. The Forward algorithm is utilized for online tool wear estimation and remaining life prognosis, and an online implementation approach is developed to reduce computational cost. Experimental results show that the approach is effective and the proposed method of duration dependency modeling leads to more accurate TWM in high speed milling.
Advances in the treatment of Clostridium difficile with fidaxomicin: a narrow spectrum antibiotic

Clostridium difficile infection, also known as C. difficile‐associated diarrhea (CDAD), is the most common cause of nosocomial diarrhea, typically initiated by the use of broad‐spectrum antibiotics that disrupt gut flora, thereby allowing C. difficile to proliferate. It is an increasing cause of morbidity and mortality, especially in hospitals and long‐term care facilities. A particularly challenging aspect to treating CDAD has been maintenance of clinical response: following initial treatment success, recurrence occurs in approximately 15–30% of patients after the first episode and up to 50–60% subsequently. Fidaxomicin, marketed as DIFICID® in the United States, is approved in multiple countries and is the first new drug to be approved for this indication in over 25 years. It is a novel, narrow spectrum antibiotic with potent bactericidal activity against C. difficile and low activity against the normal gut microbiota. In clinical trials, fidaxomicin has been shown to be noninferior in initial clinical response to CDAD compared to vancomycin, and superior in limiting recurrence and providing sustained clinical response. In this review, the development and characteristics of fidaxomicin are described.
Developing and performance evaluation of a new Arabic heavy/light stemmer

Stemming is the main step used for handling the morphologically rich languages such as Arabic. It is usually used in several fields such as Natural Language Processing, Information Retrieval (IR), and Text Mining. The goal of stemming is reducing inflected or derived words to their base (root or stem), from a generally written word form. Considering that Arabic is mainly dependent on roots and patterns to generate words, a new efficient heavy/light stemmer is developed based on the interaction between roots and patterns; yet, rich linguistic resources are involved. This stemmer provides three different outputs: individual root, a stem, and a combination of stem/root. In this paper, we highlight the performance of the developed stemmer via various experiments on both Modern Standard Arabic and Classical Arabic. In fact, the achieved accuracies are 96.93% and 96.56% for respectively the Quranic corpus "Al-Mus'haf" and NEMLAR corpus. In the context of usability testing, the effectiveness of the stemmer on IR and Part of Speech (PoS) tagging are studied. The obtained results indicate an improvement in PoS tagging by 10.98% and by 14.12% in search efficiency.
HEMORRHAGIC COMPLICATIONS AFTER PHOTODYNAMIC THERAPY FOR POLYPOIDAL CHOROIDAL VASCULOPATHY

Purpose: To evaluate the clinical features and risk factors of hemorrhagic complications in eyes with polypoidal choroidal vasculopathy (PCV) after photodynamic therapy (PDT). Methods: We retrospectively reviewed data for 91 consecutive eyes of 85 patients who underwent PDT for the treatment of PCV. The diagnosis of PCV was based on indocyanine green angiographic findings, showing a branching vascular network terminating in polypoidal swelling. The greatest linear dimension included all polypoidal lesions, leaking vascular network, and type 2 choroidal neovascularization. Results: During the follow-up period after PDT, postoperative subretinal hemorrhage was seen in 28 (30.8%) of 91 eyes. In 22 (78.6%) of these 28 eyes, subretinal hemorrhage was absorbed without treatment. In 6 eyes (21.4%), however, bleeding resulted in vitreous hemorrhage, and 2 eyes underwent pars plana vitrectomy. Although visual acuity was maintained or increased in 18 (81.8%) of 22 eyes with subretinal hemorrhage alone, it decreased significantly in 3 (50.0%) of 6 eyes with postoperative vitreous hemorrhage. Various systemic diseases and medication with an anticoagulant had no correlation with these hemorrhagic complications. Laser irradiation spot size for PDT was significantly larger in eyes with postoperative vitreous hemorrhage (P = 0.017) than in those without. Conclusion: Subretinal hemorrhage after PDT can be a common complication in patients with PCV and may have a minor effect on visual outcome. However, postoperative hemorrhage is occasionally so massive that it leads to vitreous hemorrhage and poor visual prognosis. When considering PDT for eyes with a large PCV lesion, ophthalmologists should be aware of the risk of serious hemorrhagic complications.
Social preferences, occupational choice and labor market performance

OF THE DISSERTATION Social Preferences, Occupational Choice and Labor Market Performance By EBRU ISGIN Dissertation Director: Professor Barry Sopher The first essay analyzes the role of information transparency on fairness and reciprocity in long-term labor market relationships. The main finding of the second chapter is that transparency serves as an effective mechanism to both improve worker welfare and total market efficiency. Fairness, which means that an increase in the generosity of a contract offer is reciprocated by an increase in the effort level, is a prominent concern under information transparency. When workers are fully informed about firms’ productivity levels and potential profits, firms propose higher wages that represent a relatively more fair division of total surplus. Workers respond to generous offers with high effort levels. However, workers’ response to wages is not constant and depends on the following factors. First of all, it is elevated with information transparency. That is, for given wages, workers provide more effort under full information. Secondly, it depends on whether a wage offer represents a fair share of the final surplus. The second essay analyzes the role of information transparency and communication in short-term labor market relationships. The experimental evidence shows that the level of trust and reciprocity is significantly reduced if there is no contract renewal. While information transparency was critical int the first essay with long-term relationships, it
A test of the mixture of distributions models

In this paper a direct test of the mixture of distributions model is conducted using daily stock return and trading volume of the Spanish continuous stock market for the period April 1990 to January 1996. Both the standard mixture of distributions model of Tauchen and Pitts (1983) and the modified version proposed by Andersen (1996) are estimated by the Generalized Method of Moments and tested using the overidentified restrictions. The results of the tests show the rejection of the restrictions that the standard and modified models impose on the data, that is, the dynamics of the Spanish returns and volume are not directed by a common factor, namely the flow of information, according to the specifications of the mixture models considered.
Molecular and electrophysiological characterization of transient receptor potential ion channels in the primary murine megakaryocyte

The molecular identity of platelet Ca2+ entry pathways is controversial. Furthermore, the extent to which Ca2+‐permeable ion channels are functional in these tiny, anucleate cells is difficult to assess by direct electrophysiological measurements. Recent work has highlighted how the primary megakaryocyte represents a bona fide surrogate for studies of platelet signalling, including patch clamp recordings of ionic conductances. We have now screened for all known members of the transient receptor potential (TRP) family of non‐selective cation channels in murine megakaryocytes following individual selection of these rare marrow cells using glass micropipettes. RT‐PCR detected messages for TRPC6 and TRPC1, which have been reported in platelets and megakaryocytic cell lines, and TRPM1, TRPM2 and TRPM7, which to date have not been demonstrated in cells of megakaryocytic/platelet lineage. Electrophysiological recordings demonstrated the presence of functional TRPM7, a constitutively active cation channel sensitive to intracellular Mg2+, and TRPM2, an ADP‐ribose‐dependent cation channel activated by oxidative stress. In addition, the electrophysiological and pharmacological properties of the non‐selective cation channels stimulated by the physiological agonist ADP are consistent with a major role for TRPC6 in this G‐protein‐coupled receptor‐dependent Ca2+ influx pathway. This study defines for the first time the principal TRP channels within the primary megakaryocyte, which represent candidates for Ca2+ influx pathways activated by a diverse range of stimuli in the platelet and megakaryocyte.