Miracle-dz/UniFAR-FTUs huggingface dataset:
Transcription elongator SPT6L regulates the occupancies of the SWI2/SNF2 chromatin remodelers SYD/BRM and nucleosomes at transcription start sites in Arabidopsis

Abstract Chromatin remodelers have been thought to be crucial in creating an accessible chromatin environment before transcription activation. However, it is still unclear how chromatin remodelers recognize and bind to the active regions. In this study, we found that chromatin remodelers SPLAYED (SYD) and BRAHMA (BRM) interact and co-occupy with Suppressor of Ty6-like (SPT6L), a core subunit of the transcription machinery, at thousands of the transcription start sites (TSS). The association of SYD and BRM to chromatin is dramatically reduced in spt6l and can be restored mainly by SPT6LΔtSH2, which binds to TSS in a RNA polymerase II (Pol II)-independent manner. Furthermore, SPT6L and SYD/BRM are involved in regulating the nucleosome and Pol II occupancy around TSS. The presence of SPT6L is sufficient to restore the association of the chromatin remodeler SYD to chromatin and maintain normal nucleosome occupancy. Our findings suggest that the two chromatin remodelers can form protein complexes with the core subunit of the transcription machinery and regulate nucleosome occupancy in the early transcription stage.
Generalisation of value-based attentional priority is category-specific

A large body of research suggests that previously reward-associated stimuli can capture attention. Recent evidence also suggests that value-driven attentional biases can occur for a particular category of objects. However, it is unclear how broadly these category-level attentional biases can generalise. In the present study, we examined whether value-driven attentional biases can generalise to new exemplars of a category or semantically related categories using a modified version of the value-driven attentional capture paradigm. In an initial training phase, participants searched for two categories of objects and were rewarded for correctly fixating members of one target category. In a subsequent test phase, participants searched for two new categories of objects. A new exemplar of one of the previous target categories or a member of a semantically related category could appear as a critical distractor in this phase. Participants were more likely to initially fixate the critical distractor and fixated the distractor longer when it was a new exemplar of the previously rewarded category. However, similar findings were not observed for members of semantically related categories. Together, these findings suggest that the generalisation of value-based attentional priority is category-specific.
How people diagnosed with borderline personality disorder experience relationships to oneself and to others. A qualitative in-depth study

ABSTRACT Background The first-person experiences of people diagnosed with borderline personality disorder (BPD) is an important area of research. It can support clinical and ethical practice, and nuance and expand on insights offered by diagnostic and treatment-oriented research approaches. In this study, we aimed to develop knowledge about how persons who were recently diagnosed with BPD experience being in relationships with themselves and others. Methods We conducted in-depth life-world interviews with 12 women recently diagnosed with BPD. The interviews focused on their lived experiences of relationships to self and others. All participants gave their informed consents to participate. We analysed the data with a structured approach to reflexive thematic analysis, conducted as a team-based approach. Results We extracted an overarching theme, “Reaching for firm holdings”, that is the most abstract interpretation of participants’ experiences. The five subordinate themes (“Captive of emotions”, “Keeping undeservedness at bay”, “Distrusting oneself”, “Dependence as stability” and “The uncertainty of reaching out”) are specific constituents of the overarching theme, and provide detail and variations across individual accounts. Conclusions The results suggest that the experience of relationship to self and others of people recently diagnosed with BPD entails feeling insecure, unsafe and frightened. We report five themes that describe ways participants seek to cope with this situation. The results indicate that their experiences encompass turning to others, or to objects, for feelings of safety. As such, the experience of relationship to self and others in the context of receiving a BPD diagnosis seemed to entail finding and evolving strategies to protect a vulnerable self. Self-harm, suicide attempts and addiction all seemed to be ways of handling and tolerating chaotic and frightful emotions. One major limitation of our study is that only people who identified as female were recruited to participate in the study.
Social Networks, Stigma, and Hepatitis C Care Among Women Who Inject Drugs: Findings from A Community Recruited Sample

ABSTRACT This study explores the role of perceived HCV stigma and social networks on HCV care among people who inject drugs (PWID) of both sexes, and solely among women who inject drugs (WWID). Data were from 269 HCV positive PWID, community-recruited through street-based outreach in Baltimore, MD. We defined HCV stigma based on participants’ perceptions of treatment by others and their need to conceal their HCV status. Among WWID, HCV stigma was linked with decreased odds of undergoing liver disease staging (aOR = 0.33, 95% CI: 0.13,0.85) or to have attempted to get the HCV cure (aOR = 0.39, CI: 0.16,0.97), these associations were not evident in the overall sample with both sexes. Social network characteristics were significant correlates of HCV care in the overall sample, and these associations were stronger among WWID. WWID with more HCV positive social network members had higher odds of an HCV-related healthcare visit in the prior 12 months (aOR = 4.28, CI: 1.29,14.17) and to have undergone liver disease staging (aOR = 2.85, CI: 1.01,8.05). WWID with more social network members aware of the HCV cure were more likely to report an attempt at obtaining the HCV cure (aOR = 5.25, CI: 1.85,14.89). Our results suggest complexity in the role of social networks and stigma on HCV care.
A Comparison of Solar p-Mode Parameters from MDI and GONG: Mode Frequencies and Structure Inversions

Helioseismic analysis of solar global oscillations allows investigation of the internal structure of the Sun. One important test of the reliability of the inferences from helioseismology is that the results from independent sets of contemporaneous data are consistent with one another. Here we compare mode frequencies from the Global Oscillation Network Group and Michelson Doppler Imager on board SOHO and resulting inversion results on the Sun's internal structure. The average relative differences between the data sets are typically less than 1 × 10-5, substantially smaller than the formal errors in the differences; however, in some cases the frequency differences show a systematic behavior that might nonetheless influence the inversion results. We find that the differences in frequencies are not a result of instrumental effects but are almost entirely related to the data pipeline software. Inversion of the frequencies shows that their differences do not result in any significant effects on the resulting inferences on solar structure. We have also experimented with fitting asymmetric profiles to the oscillation power spectra and find that, compared with the symmetric fits, this causes no significant change in the inversion results.
Isolation, purification and biochemical characterization of Conopomorpha cramerella farnesol dehydrogenase

In Southeast Asia, Conopomorpha cramerella (Snellen) which is commonly known as the cocoa pod borer (CPB) moth has been identified as the most detrimental pest of Theobroma cacao L. Apart from the various side effects on human health and non‐target organisms, heavily relying on synthetic pyrethroid insecticides to control CPB infestations also increases the environmental contamination risks. Thus, developing biorational insecticides that minimally affect the non‐target organism and environment by targeting the insect growth regulation process is needed to manage the pest population. In insects, juvenile hormones (JH) regulate critical biological events, especially metamorphosis, development and reproduction. Since the physiological roles of JH III vary among different organisms, the biochemical properties, especially substrate specificity and analogue inhibition, may also be different. Therefore, studies on the JH III biosynthetic pathway enzymes in both plants and insects are beneficial to discover more effective analogues. Bioinformatic analysis and biochemical characterization of a NADP+‐dependent farnesol dehydrogenase, an intermediate enzyme of the JH III pathway, from C. cramerella (CcFolDH), were described in this study. In addition, the farnesol analogues that may act as a potent analogue inhibitor for CcFolDH ware determined using in vitro enzymatic study. The phylogenetic analysis indicated that CcFolDH shared a close phylogenetic relationship to the honeybee's short‐chain dehydrogenase/reductase. The 27 kDa CcFolDH has an NADP(H) binding domain with a typical Rossmann fold and is likely a homotetrameric protein in the solution. The enzyme had a greater preference for substrate trans, trans‐farnesol and coenzyme NADP+. In terms of analogue inhibitor inhibition, hexahydroxyfarnesyl acetone showed the highest inhibition (the lowest Ki) compared to other farnesol analogues. Thus, hexahydroxyfarnesyl acetone would serve as the most potent active ingredient for future biorational pesticide management for C. cramerella infestation. Based on the bioinformatic analyses and biochemical characterizations conducted in this research, we proposed that rCcFolDH differs slightly from other reported farnesol dehydrogenases in terms of molecular weight, substrate preference, coenzymes utilization and analogue inhibitors selection.
Covers of an Elliptic Curve E and Curves in ExP1

We describe the hyperplane sections of the Severi variety of curves in E × P1 in a similar fashion to Caporaso–Harris’ seminal work. From this description we almost get a recursive formula for the Severi degrees—we get the terms, but not the coefficients. As an application, we determine the components of the Hurwitz space of simply branched covers of a genus one curve. In return, we use this characterization to describe the components of the Severi variety of curves in E × P1, in a restricted range of degrees.
Association of 25-hydroxyvitamin D with hematological profile and anthropometry in patients with glioma

SUMMARY OBJECTIVE: Gliomas are immune system suppressive tumors, and the role of vitamin D is pivotal in the immune system. This study aimed to observe if there is any significant association between the serum levels of 25-hydroxyvitamin D with hematological indices and anthropometric measurements. METHODS: A total of 75 glioma patients were included, and the information was collected on gender, age group, area, socioeconomic status, intake of vitamin D and calcium in food and supplements, skin color, sunlight exposure, body mass index, and muscle strength. A nonparametric Kendall's tau-b correlation test was performed to find a correlation between 25-hydroxyvitamin D levels and blood counts, body mass index, and muscle strength. RESULTS: The majority of patients (72%) were having low lymphocytes followed by high granulocytes and high white blood cells. The majority were having low levels of both 25-hydroxyvitamin D (84%) and calcium (73%). Patients were mainly from urban areas, and the majority belonged to middle-class families having sedentary lifestyles. The majority of patients were not taking vitamin D supplements. An insufficient amount of sunlight exposure was found in most of them. The majority of the patients were although had normal weight but weak muscle strength (74.6%). An insignificant correlation was found between 25-hydroxyvitamin D levels with the hematological indices or anthropometric measurements in brain tumor patients. CONCLUSION: Vitamin D is a powerful immune modulator, and there is a great need for sufficient amounts of sunlight exposure and vitamin D-enriched diets to prevent cancer.
Determination of source terms in a degenerate parabolic equation

In this paper, we prove Lipschitz stability results for inverse source problems relative to parabolic equations. We use the method introduced by Imanuvilov and Yamamoto in 1998 based on Carleman estimates. What is new here is that we study a class of one-dimensional degenerate parabolic equations. In our model, the diffusion coefficient vanishes at one extreme point of the domain. Instead of the classical Carleman estimates obtained by Fursikov and Imanuvilov for non degenerate equations, we use and extend some recent Carleman estimates for degenerate equations obtained by Cannarsa, Martinez and Vancostenoble. Finally, we obtain Lipschitz stability results in inverse source problems for our class of degenerate parabolic equations both in the case of a boundary observation and in the case of a locally distributed observation.
Hurdle technology based on the use of microencapsulated pepsin, trypsin and carvacrol to eradicate Pseudomonas aeruginosa and Enterococcus faecalis biofilms

Abstract The biofilm lifestyle plays a major role in the resistance and virulence of Pseudomonas aeruginosa and Enterococcus faecalis. In this study, two microencapsulated proteases (pepsin ME-PEP and trypsin ME-TRYP) were evaluated for their biofilm dispersal activity and their synergistic effect with microencapsulated carvacrol (ME-CARV). Spray-drying was used to protect enzymes and essential oil and enhance their activities. Cell count analysis proved the synergistic activity of enzymes and carvacrol treatment as biofilms were further reduced after combined treatment in comparison to ME-CARV or enzymes alone. Furthermore, results showed that sequential treatment in the order ME-TRYP - ME-PEP - ME-CARV resulted in more efficient biofilm removal with a maximum reduction of 5 log CFU mL−1 for P. aeruginosa and 4 log CFU mL−1 for E. faecalis. This study proposes that the combination of microencapsulated proteases with ME-CARV could be useful for the effective control of P. aeruginosa and E. faecalis biofilms.
DUSP22 rearrangement is associated with a distinctive immunophenotype but not outcome in patients with systemic ALK-negative anaplastic large cell lymphoma

DUSP22 rearrangement (R) has been associated with a favorable outcome in systemic ALK-negative anaplastic large cell lymphoma (ALCL). However, a recent study found that patients with DUSP22-R ALK-negative ALCL have a poorer prognosis than was reported initially. In this study, we compared the clinicopathological features and outcomes of patients with ALKnegative ALCL with DUSP22-R (n=22) versus those without DUSP22-R (DUSP22-NR; n=59). Patients with DUSP22-R ALCL were younger than those with DUSP22-NR neoplasms (P=0.049). DUSP22-R ALK-negative ALCL cases were more often positive for CD15, CD8, and less frequently expressed pSTAT3Tyr705, PD-L1, granzyme B and EMA (all P<0.05). TP63 rearrangement (TP63-R) was detected in three of the 66 (5%) ALK-negative ALCL cases tested and none of these cases carried the DUSP22-R. Overall survival of patients with DUSP22-R ALCL was similar to that of the patients with DUSP22-NR neoplasms regardless of International Prognostic Index score, stage, age, or stem cell transplantation status (all P>0.05), but was significantly shorter than that of the patients with ALK-positive ALCL (median overall survival 53 months vs. undefined, P=0.005). Five-year overall survival rates were 40% for patients with DUSP22-R ALCL versus 82% for patients with ALK-positive ALCL. We conclude that DUSP22-R neoplasms represent a distinctive subset of ALK-negative ALCL. However, in this cohort DUSP22-R was not associated with a better clinical outcome. Therefore, we suggest that current treatment guidelines for this subset of ALK-negative ALCL patients should not be modified at present.
Robustness analysis of periodic systems

Two approaches for robustness analysis of linear periodically time-varying systems are presented. In the first approach the state space matrices of the nominal system are expanded in Fourier series. The system can then be represented as an interconnection of a linear time-invariant system and an uncertainty that contains all harmonic functions in the Fourier series. Integral quadratic constraints (IQCs) can then be used to derive robustness conditions, which are equivalent to several linear matrix inequalities. In the second approach, instead of being factorized out, the harmonic terms are kept in the nominal system. Periodic IQCs are then used to characterize the uncertainties. This generally gives a lower dimensional optimization problem but with added complexity due to the fact that the system matrices are periodic.
Automated Market Makers: Mean-Variance Analysis of LPs Payoffs and Design of Pricing Functions

With the emergence of decentralized finance, new trading mechanisms called Automated Market Makers have appeared. The most popular Automated Market Makers are Constant Function Market Makers. They have been studied both theoretically and empirically. In particular, the concept of impermanent loss has emerged and explains part of the profit and loss of liquidity providers in Constant Function Market Makers. In this paper, we propose another mechanism in which price discovery does not solely rely on liquidity takers but also on an external exchange rate or price oracle. We also propose to compare the different mechanisms from the point of view of liquidity providers by using a mean / variance analysis of their profit and loss compared to that of agents holding assets outside of Automated Market Makers. In particular, inspired by Markowitz' modern portfolio theory, we manage to obtain an efficient frontier for the performance of liquidity providers in the idealized case of a perfect oracle. Beyond that idealized case, we show that even when the oracle is lagged and in the presence of adverse selection by liquidity takers and systematic arbitrageurs, optimized oracle-based mechanisms perform better than popular Constant Function Market Makers.
Adaptive fuzzy logic-controlled surface mount permanent magnet synchronous motor drive

Permanent magnet synchronous machines (PMSMs) are becoming popular in industries due to their fast transient response, high power density and high efficiency. This paper presents rotor field-oriented control of a surface mount permanent magnet synchronous motor drive with a fuzzy logic-based speed controller. A model reference adaptive fuzzy logic controller is utilised in the place of a conventional speed proportional plus integral (PI) controller. Simulation and experimental results are provided to show the applicability of artificial intelligence-based speed control of PMSMs. Results are presented for both conventional PI-based control and proposed adaptive fuzzy logic control and compared. The novelty of the paper lies in the experimental implementation of the adaptive fuzzy logic controller in vector-controlled PMSM drive.
Testing cosmology with double source lensing

Double source lensing provides a dimensionless ratio of distance ratios, a “remote viewing” of cosmology through distances relative to the gravitational lens, beyond the observer. We use this to test the cosmological framework, particularly with respect to spatial curvature and the distance duality relation. We derive a consistency equation for constant spatial curvature, allowing not only the investigation of flat vs curved but of the Friedmann-Lemaître-Robertson-Walker framework itself. For distance duality, we demonstrate that the evolution of the lens mass profile slope must be controlled to ≳ 5 times tighter fractional precision than a claimed distance duality violation. Using LensPop forecasts of double source lensing systems in Euclid and LSST surveys we also explore constraints on dark energy equation of state parameters and any evolution of the lens mass profile slope.
Discontinuities in the S-Re relations of trapezoidal and triangular cylinders

From past research, it is known that even for a very slender cylinder with aspect ratio of several hundreds, the flow remains two-dimensional only at low Reynolds number, and will become three-dimensional once a certain critical Reynolds number is exceeded. Most of the works reported are for circular and square cylinders. The present work is intended to look into wake transition phenomena that take place in the wake of two different trapezoidal and one triangular cylinders. With the experiment set up in a water tunnel, the frequency of vortices shed from trapezoidal and triangular cylinders was carefully measured using hot film anemometry. Experimental data revealed that the discontinuities in the S-Re relation, similar to those observed for circular and square cylinders and which mark the transition of the wake to Mode A and Mode B instabilities, are also present in flow past trapezoidal and triangular cylinders. However, the Reynolds numbers at which the discontinuities take place are cross-sectional geometry dependent. For Trapezoidal Cylinder 1 and 2 with a rear face 75% and 50% the length of the front face, respectively, the two discontinuities in the S-Re relation take place at Re = 152 & 173 and 143 & 176, respectively. For the Triangular Cylinder with apex pointing downstream, the first discontinuity occurs at Re = 164. Some preliminary flow visualization was also carried out to confirm the existence of the streamwise vortices associated with Mode A and B instabilities.
Determination of Majorana type-phases from the time evolution of lepton numbers

We have investigated an approach to determine the Majorana type-phases using the time evolution of lepton family numbers. The Majorana type-phases are related to the orientation of unitarity triangles for the Pontecorvo-Maki-Nakagawa-Sakata (PMNS) matrix, and the Majorana phases α 21 and α 31 . After taking the second-order time derivative of the lepton family number expectation values, the dependencies on the summation of Majorana type-phases can be determined. Thus allowing for the extraction of the orientation of the unitarity triangles and the Majorana phases. We study how to extract the Majorana type-phases and the lightest neutrino mass for three massive neutrinos, and when a neutrino is massless, i.e., m 1 , 3 = 0. Our result can be complimentary to using neutrinoless double-beta decay for determining the orientation of PMNS unitarity triangles and the Majorana phases.