Miracle-dz/UniFAR-FTUs huggingface dataset:
Nuclear and Mitochondrial Phylogenomics of the Sifakas Reveal Cryptic Variation in the Diademed Sifaka

The most comprehensive phylogenomic reconstruction to date was generated on all nominal taxa within the lemur genus Propithecus. Over 200 wild-caught individuals were included in this study to evaluate the intra and interspecific relationships across this genus. Ultraconserved Elements (UCEs) resulted in well-supported phylogenomic trees. Complete mitochondrial genomes (CMGs) largely agreed with the UCEs, except where a mitochondrial introgression was detected between one clade of the diademed sifaka (Propithecus diadema) and the Milne-Edwards sifaka (P. edwardsi). Additionally, the crowned (P. coronatus) and Von der Decken’s (P. deckeni) sifakas belonged to a single admixed lineage from UCEs. Further sampling across these two species is warranted to determine if our sampling represents a hybrid zone. P. diadema recovered two well-supported clades, which were dated and estimated as being ancient as the split between the Perrier’s (P. perrierii) and silky (P. candidus) sifakas. The reconstructed demographic history of the two clades also varied over time. We then modeled the modern ecological niches of the two cryptic P. diadema clades and found that they were significantly diverged (p < 0.01). These ecological differences result in a very limited zone of geographic overlap for the P. diadema clades (<60 km2). Niche models also revealed that the Onive River acts as a potential barrier to dispersal between P. diadema and P. edwardsi. Further taxonomic work is required on P. diadema to determine if its taxonomic status should be revised. This first genomic evaluation of the genus resolved the relationships between the taxa and the recovered cryptic diversity within one species.
First Comprehensive Analysis of Both Mitochondrial Characteristics and Mitogenome-Based Phylogenetics in the Subfamily Eumeninae (Hymenoptera: Vespidae)

Simple Summary The subfamily Eumeninae comprises more than 3900 described species and eumenine mitochondrial analyses are almost absent. In order to provide further evidence toward understanding the relationships within the subfamily, the characteristics of 54 eumenine mitogenomes were comparatively analyzed, among which 52 mitogenomes are newly annotated. Meanwhile, using both Maximum-likelihood (ML) and Bayesian inference (BI), comprehensive phylogenetic relationship in the subfamily were investigated based on two mitochondrial datasets. Abstract The subfamily Eumeninae plays a significant role in the biological control of agricultural pests. However, the characteristics of eumenine mitogenomes that are important molecular markers for phylogenetics are not clearly revealed. Here, 52 eumenine mitogenomes are newly sequenced and annotated, and the phylogenetic relationships of the subfamily are comprehensively analyzed based on 87 vespid mitogenomes. Through the comparative analysis of the 54 eumenine mitogenomes, the gene compositions of about one half of the 54 species match with ancestral insect mitogenome, and remaining others contain two trnM which are highly similar, with 51.86% (Eumenes tripunctatus) to 90.65% (Pseumenes nigripectus) sequence identities, which is unique among the reported mitogenomes of the family Vespidae. Moreover, the translocation trnL1 upstream of nad1 is a common rearrangement event in all eumenine mitogenomes. The results of phylogenetic analyses support the paraphyly of the subfamily Eumeninae and the tribe Odynerini, respectively, and the monophyly of the tribe Eumenini, and verify that the tribe Zethini is a valid subfamily Zethinae. In this study, the relationships between some genera such as Allorhynchium and Pararrhynchium or the taxonomic status of the subgenera such as Eremodynerus and Dirhynchium are found to be confusing and there should be further inquiry with more samples.
Inexact Graph Matching Using Symbolic Constraints

Relational graphs are a fundamental type of scene representation for medium and high level computer vision tasks. They provide a generic way of encoding entities and relationships. The comparison and matching of such graphs is an important and challenging problem under the conditions of uncertainty and corruption which exist in most vision problems. In this thesis a method for matching relational graphs is developed which is based on symbolic constraints. The topology of the graph relations is used to calculate the consistency of a particular match using a Bayesian probability model of the processes at work in the matching process. The result is a global consistency criterion which measures the quality of match. A discrete relaxation technique is used to locate the optimal mapping between graphs using a MAP update rule. The technique is evaluated using both real-world image data and simulated graphs. Three methods of eliminating spurious elements from the graphs are also studied. The first method involves a constraint-filtering method which is applied after matching has taken place. The second method is an optimisation technique in which noise elements are identified and labelled during the matching process. The final method involves the dynamic reconfiguration of the graphs to remove noise elements during the matching phase. Detailed evaluations of these methods are performed on simulated data. A theoretical analysis of the criterion is carried out which allows prediction of the expectation value of the criterion at a given level of graph corruption. The performance of the symbolic criterion is compared to that of other alternatives reported in the literature. Finally the symbolic methods developed earlier are extended both to the use of probabilistic relaxation to match relational graphs, and to the matching of hierarchical graphs.
Predicting The Energy Consumption Level of Java Classes in Android Apps: An Exploratory Analysis

Mobile applications usage has considerably increased since the last decade. Successful apps need to make the users feel comfortable while using them, thus demanding high-quality design and implementation. One of the most influencing factors for user experience is battery consumption, which should have the minimum possible impact on the battery. The current body of knowledge on energy consumption measurement only reports approaches relying on complex instrumentation or stressing the application with many test scenarios, thus making it hard to measure energy consumption in practice. In this work, we explore the performance of machine learning to predict the energy consumption level of JAVA classes in Android apps, leveraging only a set of structural properties extracted via source code analysis, without requiring any hardware measurements tools or executing the app at all. The preliminary results show the poor performance of learning-based estimation models, likely caused by (1) an insufficient amount of training data, (2) a limited feature set, and (3) an inappropriate way to label the dependent variable. The paper concludes by presenting the limitations of the experimented models and the possible strategies to address them.
Relation between the Genetic Variants of SLC47A1 (MATE1) and the Response to Metformin Therapy in Iraqi Women with Polycystic Ovarian Syndrome

Background: Metformin is widely used in polycystic ovary syndrome (PCOS), nevertheless, the treatment responsiveness reveals individual variation in patients with PCOS. Multidrug and toxins extrusion protein (MATE1) mediates metformin excretion in kidney and bile. MATE1 is encoded by SLC47A1 gene. In this study the single-nucleotide polymorphism (SNP) (rs1961669 A>G) was analyzed in an attempt to investigate the clinical, hormonal and biochemical effects of three months metformin treatment in women with polycystic ovary syndrome and to study the relation between MATE1 (SLC47A1) gene polymorphism and the response to metformin. Patients and Methods: This study is a prospective group study; 231 women with PCOS were enrolled. All participated women with age range (18-40) were starting metformin tablet 500 mg per oral three times daily. Blood samples were taken from eligible patients to perform genetic analysis and estimation of follicle stimulating hormone, luteinizing hormone, total testosterone, fasting insulin, HbA1c, fasting blood glucose, sex hormone binding globulin and lipid profile. Results: The study showed that SLC47A1 (rs1961669) (A>G) gene polymorphism has nonsignificant association with metformin response in PCOS. The comparison in demographic and biochemical parameters between pre and post metformin treatment results showed no improvement in clinical, hormonal and biochemical parameters. Conclusion: SLC47A1 (rs1961669) (A>G) gene polymorphism had no association with clinical, hormonal and biochemical response to metformin in Iraqi women with polycystic ovarian syndrome.
A Study Of The Effects Of High School Scheduling Systems On Achievement Rates, Attendance Rates, And Dropout Rates

This study attempted to determine if the type of class schedule (traditional, A/B block, or accelerated block) used in Texas public high schools significantly affects students' achievement results, attendance rates and dropout rates. One thousand four hundred ninety (1490) Texas high school principals were surveyed to determine the type of schedule currently in use on each campus, the type of schedule previously used on each campus, the length of time the current schedule has been in place on each campus, and the length of time that the previous schedule was used on each campus. This study is particularly significant in that this research provides information to assist principals in determining if block scheduling is instrumental in improving achievement in reading and mathematics, in improving attendance and in lowering dropout rates. The results of the study indicated that the use of a particular type of schedule: traditional, A/B block, or accelerated block is not directly correlated to improved achievement, attendance, or dropout rates. An expectation that the implementation of a traditional, A/B block, or accelerated block schedule will be the sole factor to cause improved student achievement, improved attendance rates or improved dropout rates is inappropriate. Ultimately, campus and districts officials must assure that effective teaching practices are occurring on each campus, regardless of the schedule type. Currently, a projected (Texas) state education funding shortfall is causing school district administrators to review cost-saving options for the 2003 - 2004 fiscal year. There is discussion in many districts regarding the fact that traditional scheduling is more economical than A/B block or accelerated block scheduling. The results of this study indicate that the decision to move campuses from A/B block or accelerated block to traditional scheduling might be made as a cost-saving move without negatively impacting student achievement, attendance rates or dropout rates.
Arabic Language Production: Challenges for Indonesian Adult and Children Learners

Many learners of foreign language face difficulties in the process of language acquisition. They are required to study his second language seriously and passionately, but in practice there are many obstacles or difficulties encountered during the process of language production. They may encounter some difficulty in writing/speaking or reading/listening. The purpose of this study is to identify and explore the difficulties in the production process of Arabic. The study uses descriptive methods and collects data through direct techniques, namely: observing and interviewing the learners in the learning process. It identifies stages in which learners find learning difficulties in both composing perfect sentences and understanding Arabic speech. These difficulties occur when learners are at the beginning of learning Arabic as a foreign language. Children beginner learner face difficulty in the message stage, while adult beginner learners think that the difficulty occurs in the functional stage.
Reply on RC2

Major concerns: On channelization threshold: 0.05 km2 does not always outline better hydrography. Because uncertainty remains in headwater channel initialization threshold, and if you read earlier HydroSHEDS documentations by Lehner’s group, and you will find it says often times threshold smaller than 100 grid cells (100*90m*90m) will introduce a lot of uncertainty. So, can the authors provide more justification on why using 0.05km2? How about the uncertainty it provided? What if the 726M lines mean just “more” channels, but not “better” channels? (related to this, what does it mean by saying “we address the allimportant issues of headwaters” in Line 70? Is it related to the 0.05 km2 threshold? )
Exclusive Dealing and Entry by Competing Two-Sided Platforms

We study competition between horizontally differentiated platforms offering exclusive and non-exclusive contracts to one side of the market (content providers). The introduction of non-exclusive contracts in addition to exclusive contracts softens the competition for content providers between platforms, as they have more tools to extract content providers’ surplus. Users on the other side (consumers) pay the same price that they would pay in the exclusive-only game but gain access to new content provided by multi-homing content providers, increasing their surplus. Multi-homing content providers’ surplus increases, while it decreases for those who single-home. Platforms charge more to exclusive and non-exclusive content providers, increasing their profits. As platform competition increases, platforms’ profits increase if the network benefit on the consumers’ side is high, so that the price effect dominates the market share effect. Finally, we show that platforms cannot deter entry by offering exclusive–non-exclusive contracts. In certain circumstances, platforms will jointly deviate from the exclusive–non-exclusive game and offer only exclusive prices in order to deter entry.
Effects ofCorneal StromalLensCollagenCross-LinkingRegraft on Corneal Biomechanics

Background. Corneal collagen cross-linking (CXL) therapy, a method that uses a combination of riboavin and ultraviolet-A light (UVA), can promote the formation of covalent cross-linking of amino acid residues of corneal collagen and enhance the hardness of the cornea. In this study, we explored the eects of corneal stromal lens collagen cross-linking regraft on corneal biomechanics. Methods. A total of 15 New Zealand white rabbits were divided into 3 groups: normal control group (group A), SMILE+ uncrosslinked lens implantation group (Group B), and SMILE+ cross-linking lens implantation group (group C). e design parameters of SMILE surgery were as follows: the corneal cap was 120 um thick, the lens diameter was 6.5mm, and the diopter was -6.0D. Riboavin and ultraviolet-A (UVA) were used as corneal stromal lens CXL, which was implanted into the allogeneic rabbit corneal stromal bag 24 hours after the operation. Postoperative corneal thickness (CCT), refraction, AS-OCT, and corneal biomechanics were performed before and then at 1 and 3 months after the operation. Results. All corneas appeared transparent and smooth 3 months after surgery. e corneal thicknesses of both group B and group C were lower than those before the operation. e corrected refraction of group B and group C after lens implantation was also lower than the expected corrected power; there was no signicant dierence between the two groups (P> 0.05). AS-OCT results showed an uneven surface and thickness of the corneal stromal lens in two eyes of group B. Moreover, corneal elastic deformation increased with intraocular pressure in each group; displacement from large to small was group B> group C and> group A. e creep from large to small was group B> group C> group A. e berboard layers of groups B and C were disordered, and there were a few autophagosomes in the broblasts of group B by transmission electronmicroscopy (TEM). Conclusions. Allograft graft of corneal stromal lens collagen cross-linked can signicantly increase the biomechanical properties of the cornea.
Film as a gateway to teaching about slavery through historical empathy: a case study using 12 Years a Slave (B40-HistEducResJ-19-6)

We have studied how eliciting historical empathy in a class of 13th grade students through using the film 12 Years a Slave (McQueen, 2013) supported their in-depth understanding of slavery in nineteenth-century USA. Historical empathy is one of the core elements of the new curricular reform implemented from 2020 in Norway, and it is believed to have potential to strengthen: (1) students’ future citizenship and participation in democratic and multicultural societies; and (2) students’ in-depth understanding of history. We implemented a five-week lesson plan with different activities based around the film, and used students’ assignments to evaluate their feelings about the lessons and their historical understanding of slavery. The results confirmed the potential of film to enhance historical empathy when the screening is well prepared and combined with relevant activities. Students demonstrated a high level of engagement and managed to perform complex tasks. Both their ability to contextualise and to ‘care’ improved. Particularly, History Education Research Journal https://doi.org/10.14324/HERJ.19. 1.06 Film as a gateway to teaching about slavery through historical empathy 2 students’ historical understanding of slavery was boosted by the group conversations and the dialogic nature of the activities in the classroom. In addition, we observed a greater positive influence on boys’ achievements compared with girls’ – a finding which is interesting in a wider educational context and which needs further exploration.
Unilateral Carbon Policies and Multilateral Coalitions

Kortum and Weisbach (2021) propose a general equilibrium model for carbon taxation and derive the optimal policy as a function of marginal damages from emissions. This paper serves as an extension of Kortum and Weisbach by combining the general structure of Kortum and Weisbach with the Eaton and Kortum (2002) model of trade. Our results generalize Kortum and Weisbach to a multi-country world where the coalition consists of many heterogeneous countries. Like Kortum and Weisbach, our optimal policy consists of i) an extraction tax, ii) a partial border adjustment that partially shifts the tax imposition downstream and reduces leakage, and iii) an export policy that simultaneously exploits inelastic demand for goods amongst noncoalition countries and expands the export margin. Because the export policy functions as an external penalty incentivizing participation, we interpret coalitions implementing the optimal policy as climate clubs akin to those orignally proposed by Nordhaus (2015). We find that coalitions that implement the optimal unilateral policy can be unstable and that coalition instability has a considerable impact on the effectiveness of the optimal unilateral policy in reducing global emissions. I would like to express my sincerest gratitude to Professor Kortum, whose invaluable assistance, support, and mentorship over the past two years as my professor, research advisor, and thesis advisor made this paper possible. I would also like to thank my parents, sister, uncle, grandparents, and friends, including Chris, Robert, Mark, Daniel, and Michelle, who supported and encouraged me throughout this process. Finally, I’d like to thank Professor Patrick Devlin, who taught me to find curiosity at the intersection of rigor and intuition, and the late Bob Turansky, who taught me that knowledge without understanding is hollow. All errors are my own.
Calcium-Dependent Mechanism Protein Kinase C and Is Secreted by a HMGB1 Is Phosphorylated by Classical

High-mobility group box 1 protein (HMGB1) has been studied as a key mediator of inﬂammatory diseases, including sepsis. Regulating secretion is important in the control of HMGB1-mediated inﬂammation. Previously, it was shown that HMGB1 needs to be phosphorylated for secretion. In this study, we show that HMGB1 is phosphorylated by the classical protein kinase C (cPKC) and is secreted by a calcium-dependent mechanism. For this study, RAW264.7 cells and human peripheral blood monocytes were treated with PI3K inhibitors wortmannin, LY294002, and ZSTK474, resulting in inhibition of LPS-stimulated HMGB1 secretion, whereas inhibitors of NF- (cid:1) B and MAPKs p38 and ERK showed no inhibition. Akt inhibitor IV and mammalian target of rapamycin inhibitor rapamycin did not inhibit HMGB1 secretion. However, the PKC inhibitors Go¨6983 (broad-spectrum PKC), Go¨6976 (cPKC), and Ro-31-7549 (cPKC) and phosphoinositide-dependent kinase 1 inhibitor, which results in protein kinase C (PKC) inhibition, inhibited LPS-stimulated HMGB1 secretion. PKC activators, PMA and bryostatin-1, enhanced HMGB1 secretion. In an in vitro kinase assay, HMGB1 was phosphorylated by recombinant cPKC and by puriﬁed nuclear cPKC from LPS-stimulated RAW264.7 cells, but not by casein kinase II or cdc2. HMGB1 secretion was also induced by the calcium ionophore A23187 and inhibited by the Ca 2 (cid:2) chelators BAPTA-AM and EGTA. These ﬁndings support a role for Ca 2 (cid:2) -dependent PKC in HMGB1 secretion. Thus, we propose that cPKC is an effector kinase of HMGB1 phosphorylation in LPS-stimulated monocytes and PI3K-phosphoinositide-dependent kinase 1 may act in concert to control HMGB1 secretion independent of the NF- (cid:1) B, p38, and ERK pathways. The Journal of Immunology, 2009, 182: 5800–5809.
On the Economic Origins of Restricting Women’s Promiscuity

This paper studies the origins and function of customs and norms that intend to keep women from being promiscuous. Using large-scale survey data from more than 100 countries, I test the anthropological theory that a particular form of preindustrial subsistence – pastoralism – favored the adoption of such customs and norms. Pastoralism was characterized by heightened paternity uncertainty due to frequent and often extended periods of male absence from the settlement, implying larger incentives to imposing restrictions on women’s sexuality. The paper shows that women from historically more pastoral societies (i) are subject to stronger antiabortion attitudes; (ii) are more likely to have undergone infibulation, the most invasive form of female genital cutting; (iii) are more restricted in their freedom of mobility; and (iv) adhere to more restrictive norms about women’s promiscuity. Instrumental variable estimations that make use of the ecological determinants of pastoralism support a causal interpretation of the results. I also provide evidence that the mechanism behind these patterns is indeed paternity uncertainty, rather than male dominance, per se, or historical economic development. JEL classification: I15, N30, Z13
Portal Explaining the paradoxical rejection-aggression link : The mediating effects of hostile intent attributions , anger , and decreases in state self-esteem on peer rejection-related aggression in youth

People are strongly motivated to feel accepted by others. Yet when faced with acute peer rejection they often aggress against the very peers they desire acceptance from, which may lead to further rejection. The present experiment tests three potential mediators of aggressive responses to acute peer rejection in the critical developmental stage of early adolescence. Participants (N = 185, M age = 11.5 years) completed personal profiles that were allegedly evaluated online by peers. After receiving negative or neutral peer feedback, participants could aggress against the same peers who had evaluated them. Rejected participants attributed more hostile intent to the peers, were angrier, showed a greater reduction in state selfesteem, and were more aggressive. Mediational analyses showed that hostile intent attributions mediated the acute peer rejection–aggression relationship, whereas increases in anger and decreases in state self-esteem did not. Thus, acute peer rejection evokes hostile intent attributions that, in turn, lead to aggressive reactions.