Miracle-dz/UniFAR-FTUs huggingface dataset:
egr-4, a target of EGFR signaling, is required for the formation of the brain primordia and head regeneration in planarians

During the regeneration of freshwater planarians, polarity and patterning programs play essential roles in determining whether a head or a tail regenerates at anterior or posterior-facing wounds. This decision is made very soon after amputation. The pivotal role of the Wnt/β-catenin and Hh signaling pathways in re-establishing anterior-posterior (AP) polarity has been well documented. However, the mechanisms that control the growth and differentiation of the blastema in accordance with its AP identity are less well understood. Previous studies have described a role of Smed-egfr-3, a planarian epidermal growth factor receptor, in blastema growth and differentiation. Here, we identify Smed-egr-4, a zinc-finger transcription factor belonging to the early growth response gene family, as a putative downstream target of Smed-egfr-3. Smed-egr-4 is mainly expressed in the central nervous system and its silencing inhibits anterior regeneration without affecting the regeneration of posterior regions. Single and combinatorial RNA interference to target different elements of the Wnt/β-catenin pathway, together with expression analysis of brain- and anterior-specific markers, revealed that Smed-egr-4: (1) is expressed in two phases – an early Smed-egfr-3-independent phase and a late Smed-egfr-3-dependent phase; (2) is necessary for the differentiation of the brain primordia in the early stages of regeneration; and (3) that it appears to antagonize the activity of the Wnt/β-catenin pathway to allow head regeneration. These results suggest that a conserved EGFR/egr pathway plays an important role in cell differentiation during planarian regeneration and indicate an association between early brain differentiation and the proper progression of head regeneration.
Massive MIMO: An Introduction

Demand for wireless throughput, both mobile and fixed, will always increase. One can anticipate that, in five or ten years, millions of augmented reality users in a large city will want to transmit and receive 3D personal high-definition video more or less continuously, say 100 megabits per second per user in each direction. Massive MIMO-also called Large-Scale Antenna Systems-is a promising candidate technology for meeting this demand. Fifty-fold or greater spectral efficiency improvements over fourth generation (4G) technology are frequently mentioned. A multiplicity of physically small, individually controlled antennas performs aggressive multiplexing/demultiplexing for all active users, utilizing directly measured channel characteristics. Unlike today's Point-to-Point MIMO, by leveraging time-division duplexing (TDD), Massive MIMO is scalable to any desired degree with respect to the number of service antennas. Adding more antennas is always beneficial for increased throughput, reduced radiated power, uniformly great service everywhere in the cell, and greater simplicity in signal processing. Massive MIMO is a brand new technology that has yet to be reduced to practice. Notwithstanding, its principles of operation are well understood, and surprisingly simple to elucidate.
XQBE (XQuery By Example): A visual interface to the standard XML query language

The spreading of XML data in many contexts of modern computing infrastructures and systems causes a pressing need for adequate XML querying capabilities; to address this need, the W3C is proposing XQuery as the standard query language for XML, with a language paradigm and a syntactic flavor comparable to the SQL relational language. XQuery is designed for meeting the requirements of skilled database programmers; its inherent complexity makes the new language unsuited to unskilled users.In this article we present XQBE (XQuery By Example), a visual query language for expressing a large subset of XQuery in a visual form. In designing XQBE, we targeted both unskilled users and expert users wishing to speed up the construction of their queries; we have been inspired by QBE, a relational language initially proposed as an alternative to SQL, which is supported by Microsoft Access. QBE is extremely successful among users who are not computer professionals and do not understand the subtleties of query languages, as well as among professionals who can draft their queries very quickly.According to the hierarchical nature of XML, XQBE's main graphical elements are trees. One or more trees denote the documents assumed as query input, and one tree denotes the document produced by the query. Similar to QBE, trees are annotated so as to express selection predicates, joins, and the passing of information from the input trees to the output tree.This article formally defines the syntax and semantics of XQBE, provides a large set of examples, and presents a prototype implementation.
New insights into the maternal to zygotic transition

The initial phases of embryonic development occur in the absence of de novo transcription and are instead controlled by maternally inherited mRNAs and proteins. During this initial period, cell cycles are synchronous and lack gap phases. Following this period of transcriptional silence, zygotic transcription begins, the maternal influence on development starts to decrease, and dramatic changes to the cell cycle take place. Here, we discuss recent work that is shedding light on the maternal to zygotic transition and the interrelated but distinct mechanisms regulating the onset of zygotic transcription and changes to the cell cycle during early embryonic development.
Effect of Inhaled Glucocorticoids in Childhood on Adult Height

HW Kelly, AL Sternberg, R Lescher; CAMP Research Group. N Engl J Med. 2012;367(10):904–912 Inhaled glucocorticoids (ICS) have been shown to have a temporary decrease in linear growth velocity in children. The effect of ICS on adult height has not been well defined. Participants (943 of 1041) in the Childhood Asthma Management Program study were enrolled between December 1993 and September 1995. They were between 5 and 13 years of …
Novel Heterotypic Rox Sites for Combinatorial Dre Recombination Strategies

Site-specific recombinases (SSRs) such as Cre are widely used in gene targeting and genetic approaches for cell labeling and manipulation. They mediate DNA strand exchange between two DNA molecules at dedicated recognition sites. Precise understanding of the Cre recombination mechanism, including the role of individual base pairs in its loxP target site, guided the generation of mutant lox sites that specifically recombine with themselves but not with the wild type loxP. This has led to the development of a variety of combinatorial Cre-dependent genetic strategies, such as multicolor reporters, irreversible inversions, or recombination-mediated cassette exchange. Dre, a Cre-related phage integrase that recognizes roxP sites, does not cross-react with the Cre-loxP system, but has similar recombination efficiency. We have previously described intersectional genetic strategies combining Dre and Cre. We now report a mutagenesis screen aimed at identifying roxP base pairs critical for self-recognition. We describe several rox variant sites that are incompatible with roxP, but are able to efficiently recombine with themselves in either purified systems or bacterial and eukaryotic tissue culture systems. These newly identified rox sites are not recognized by Cre, thus enabling potential combinatorial strategies involving Cre, Dre, and target loci including multiple loxP and roxP variants.
Daily Activity of the Housefly, Musca domestica, Is Influenced by Temperature Independent of 3′ UTR period Gene Splicing

Circadian clocks orchestrate daily activity patterns and free running periods of locomotor activity under constant conditions. While the first often depends on temperature, the latter is temperature-compensated over a physiologically relevant range. Here, we explored the locomotor activity of the temperate housefly Musca domestica. Under low temperatures, activity was centered round a major and broad afternoon peak, while high temperatures resulted in activity throughout the photophase with a mild midday depression, which was especially pronounced in males exposed to long photoperiods. While period (per) mRNA peaked earlier under low temperatures, no temperature-dependent splicing of the last per 3ʹ end intron was identified. The expression of timeless, vrille, and Par domain protein 1 was also influenced by temperature, each in a different manner. Our data indicated that comparable behavioral trends in daily activity distribution have evolved in Drosophila melanogaster and M. domestica, yet the behaviors of these two species are orchestrated by different molecular mechanisms.
Towards full-body haptic feedback: the design and deployment of a spatialized vibrotactile feedback system

This paper presents work we have done on the design and implementation of an untethered system to deliver haptic cues for use in immersive virtual environments through a body-worn garment. Our system can control a large number of body-worn vibration units, each with individually controllable vibration intensity. Several design iterations have helped us to refine the system and improve such aspects as robustness, ease of donning and doffing, weight, power consumption, cable management, and support for many different types of feedback units, such as pager motors, solenoids, and muffin fans. In addition, experience integrating the system into an advanced virtual reality system has helped define some of the design constraints for creating wearable solutions, and to further refine our implementation.
MetaImprint: an information repository of mammalian imprinted genes

Genomic imprinting is a complex genetic and epigenetic phenomenon that plays important roles in mammalian development and diseases. Mammalian imprinted genes have been identified widely by experimental strategies or predicted using computational methods. Systematic information for these genes would be necessary for the identification of novel imprinted genes and the analysis of their regulatory mechanisms and functions. Here, a well-designed information repository, MetaImprint (http://bioinfo.hrbmu.edu.cn/MetaImprint), is presented, which focuses on the collection of information concerning mammalian imprinted genes. The current version of MetaImprint incorporates 539 imprinted genes, including 255 experimentally confirmed genes, and their detailed research courses from eight mammalian species. MetaImprint also hosts genome-wide genetic and epigenetic information of imprinted genes, including imprinting control regions, single nucleotide polymorphisms, non-coding RNAs, DNA methylation and histone modifications. Information related to human diseases and functional annotation was also integrated into MetaImprint. To facilitate data extraction, MetaImprint supports multiple search options, such as by gene ID and disease name. Moreover, a configurable Imprinted Gene Browser was developed to visualize the information on imprinted genes in a genomic context. In addition, an Epigenetic Changes Analysis Tool is provided for online analysis of DNA methylation and histone modification differences of imprinted genes among multiple tissues and cell types. MetaImprint provides a comprehensive information repository of imprinted genes, allowing researchers to investigate systematically the genetic and epigenetic regulatory mechanisms of imprinted genes and their functions in development and diseases.
The Nonmuscle Myosin Phosphatase PP1β (flapwing) Negatively Regulates Jun N-Terminal Kinase in Wing Imaginal Discs of Drosophila

Drosophila flapwing (flw) codes for serine/threonine protein phosphatase type 1β (PP1β). Regulation of nonmuscle myosin activity is the single essential flw function that is nonredundant with the three closely related PP1α genes. Flw is thought to dephosphorylate the nonmuscle myosin regulatory light chain, Spaghetti Squash (Sqh); this inactivates the nonmuscle myosin heavy chain, Zipper (Zip). Thus, strong flw mutants lead to hyperphosphorylation of Sqh and hyperactivation of nonmuscle myosin activity. Here, we show genetically that a Jun N-terminal kinase (JNK) mutant suppresses the semilethality of a strong flw allele. Alleles of the JNK phosphatase puckered (puc) genetically enhance the weak allele flw1, leading to severe wing defects. Introducing a mutant of the nonmuscle myosin-binding subunit (Mbs) further enhances this genetic interaction to lethality. We show that puc expression is upregulated in wing imaginal discs mutant for flw1 and pucA251 and that this upregulation is modified by JNK and Zip. The level of phosphorylated (active) JNK is elevated in flw1 enhanced by puc. Together, we show that disruption of nonmuscle myosin activates JNK and puc expression in wing imaginal discs.
The maternal nucleolus plays a key role in centromere satellite maintenance during the oocyte to embryo transition

The oocyte (maternal) nucleolus is essential for early embryonic development and embryos originating from enucleolated oocytes arrest at the 2-cell stage. The reason for this is unclear. Surprisingly, RNA polymerase I activity in nucleolus-less mouse embryos, as manifested by pre-rRNA synthesis, and pre-rRNA processing are not affected, indicating an unusual role of the nucleolus. We report here that the maternal nucleolus is indispensable for the regulation of major and minor satellite repeats soon after fertilisation. During the first embryonic cell cycle, absence of the nucleolus causes a significant reduction in major and minor satellite DNA by 12% and 18%, respectively. The expression of satellite transcripts is also affected, being reduced by more than half. Moreover, extensive chromosome bridging of the major and minor satellite sequences was observed during the first mitosis. Finally, we show that the absence of the maternal nucleolus alters S-phase dynamics and causes abnormal deposition of the H3.3 histone chaperone DAXX in pronuclei of nucleolus-less zygotes.
The microarchitecture of FPGA-based soft processors

As more embedded systems are built using FPGA platforms, there is an increasing need to support processors in FPGAs. One option is the soft processor, a programmable instruction processor implemented in the reconfigurable logic of the FPGA. Commercial soft processors have been widely deployed, and hence we are motivated to understand their microarchitecture. We must re-evaluate microarchiteture in the soft processor context because an FPGA platform is significantly different than an ASIC platform---for example, the relative speed of memory and logic is quite different in the two platforms, as is the area cost. In this paper we present an infrastructure for rapidly generating RTL models of soft processors, as well as a methodology for measuring their area, performance, and power. Using our automatically-generated soft processors we explore the microarchitecture trade-off space including: (i) hardware vs software multiplication support; (ii) shifter implementations; and (iii) pipeline depth, organization, and forwarding. For example, we find that a 3-stage pipeline has better wall-clock-time performance than deeper pipelines, despite lower clock frequency. We also compare our designs to Altera's NiosII commercial soft processor variations and find that our automatically generated designs span the design space while remaining very competitive.
HIV/AIDS misconceptions may be associated with condom use among black South Africans: an exploratory analysis

In South Africa, approximately 20% of 15–49-year-olds are infected with HIV. Among black South Africans, high levels of HIV/AIDS misconceptions (e.g. HIV is manufactured by whites to reduce the black African population; AIDS is caused by supernatural forces or witchcraft) may be barriers to HIV prevention. We conducted a cross-sectional study of 150 young black adults (aged 18–26; 56% males) visiting a public clinic for sexually transmitted infections, to investigate whether HIV/AIDS misconceptions were related to low condom use in main partner relationships. We assessed agreement with HIV/AIDS misconceptions relating to the supernatural (e.g. witchcraft as a cause of HIV) and to genocide (e.g. the withholding of a cure). In multivariate models, agreement that ‘Witchcraft plays a role in HIV transmission’ was significantly related to less positive attitudes about condoms, less belief in condom effectiveness for HIV prevention, and lower intentions to use condoms among men. The belief that ‘Vitamins and fresh fruits and vegetables can cure AIDS’ was associated with lower intentions among men to use condoms. Women who endorsed the belief linking HIV to witchcraft had a higher likelihood of unprotected sex with a main partner, whereas women who endorsed the belief that a cure for AIDS was being withheld had a lower likelihood of having had unprotected sex. Knowledge about distinct types of HIV/AIDS misconceptions and their correlates can help in the design of culturally appropriate HIV-prevention messages that address such beliefs.
Clinicopathological Characteristics of Pernicious Anemia: A Study of 300 Patients in Turkey

Aims: Our study was undertaken to examine the laboratory and clinical features of pernicious anemia patients presenting initially at the Turgut Ozal Medical Center, which serves as an important tertiary health center in Eastern Anatolia. Study Design: Among patients evaluated for etiology of anemia, we analysed the clinicopathological characteristics of 300 (158 females and 142 males) patients with pernicious anemia retrospectively. Place and Duration of Study: Department of Internal Medicine and Division of Hematology, Inonu University School of Medicine, between 1996 and July 2011. Methodology: Full blood counts, thyroid hormone levels, liver function tests and LDH levels Original Research Article British Journal of Medicine & Medical Research, 4(3): 807-815, 2014 808 were reviewed for 300 patients with pernicious anemia retrospectively. Peripheral blood smears and bone marrow biopsies were reviewed by a hematologist. Endoscopic examination and ultrasonographic inspection were performed for atrophic gastritis, gallbladder stones and hepatosplenomegaly for all patients. Laboratory values, ages, signs and symptoms of patients at the time of diagnosis were compared between genders. Results: The mean age of the female patients was 50.56 ± 17.75 years (17–84), while that of the male patients was 57.24 ± 15.78 (20–95) years. At the time of diagnosis, the male patients were older than the females (p = 0.002). LDH levels were significantly higher for females (p = 0.043). The incidence of gallstones was significantly higher in females (25.4%) than in males (10.7%) (p = 0,001). Pancytopenia was defined as a hemoglobin level lower than 10 gr/dl, leukocytes lower than 1.500/μL and platelets lower than 150.000/μL and the incidence of pancytopenia was 41.3% (n = 65) and 50.7% (n = 71) in the female and male patients, respectively, and the difference was not statistically significant. There was no statistically significant difference for frequency of thyroid disease or symptoms and signs at the time of diagnosis between genders. Conclusions: Pernicious anemia is not a disease of only elderly women; it can be seen in both men and women of younger ages. It is seen nearly as often in women as in men. Gallstones and abnormal thyroid activity can be observed at these patients at the time of diagnosis; therefore, these findings should be considered.
Initiation of Hippo signaling is linked to polarity rather than to cell position in the pre-implantation mouse embryo

In the mouse embryo, asymmetric divisions during the 8-16 cell division generate two cell types, polar and apolar cells, that are allocated to outer and inner positions, respectively. This outer/inner configuration is the first sign of the formation of the first two cell lineages: trophectoderm (TE) and inner cell mass (ICM). Outer polar cells become TE and give rise to the placenta, whereas inner apolar cells become ICM and give rise to the embryo proper and yolk sac. Here, we analyze the frequency of asymmetric divisions during the 8-16 cell division and assess the relationships between cell polarity, cell and nuclear position, and Hippo signaling activation, the pathway that initiates lineage-specific gene expression in 16-cell embryos. Although the frequency of asymmetric divisions varied in each embryo, we found that more than six blastomeres divided asymmetrically in most embryos. Interestingly, many apolar cells in 16-cell embryos were located at outer positions, whereas only one or two apolar cells were located at inner positions. Live imaging analysis showed that outer apolar cells were eventually internalized by surrounding polar cells. Using isolated 8-cell blastomeres, we carefully analyzed the internalization process of apolar cells and found indications of higher cortical tension in apolar cells than in polar cells. Last, we found that apolar cells activate Hippo signaling prior to taking inner positions. Our results suggest that polar and apolar cells have intrinsic differences that establish outer/inner configuration and differentially regulate Hippo signaling to activate lineage-specific gene expression programs.
Polycomb and Trithorax Group Genes in Drosophila

Polycomb group (PcG) and Trithorax group (TrxG) genes encode important regulators of development and differentiation in metazoans. These two groups of genes were discovered in Drosophila by their opposing effects on homeotic gene (Hox) expression. PcG genes collectively behave as genetic repressors of Hox genes, while the TrxG genes are necessary for HOX gene expression or function. Biochemical studies showed that many PcG proteins are present in two protein complexes, Polycomb repressive complexes 1 and 2, which repress transcription via chromatin modifications. TrxG proteins activate transcription via a variety of mechanisms. Here we summarize the large body of genetic and biochemical experiments in Drosophila on these two important groups of genes.
Topological crossover for the permutation representation

Topological crossovers are a class of representation-independent operators that are well-defined once a notion of distance over the solution space is defined. In this paper we explore how the topological framework applies to the permutation representation and in particular analyze the consequences of having more than one notion of distance available. Also, we study the interactions among distances and build a rational picture in which pre-existing recombination/crossover operators for permutation fit naturally. Lastly, we also analyze the application of topological crossover to TSP.
The role of T-cadherin in axonal pathway formation in neocortical circuits

Cortical efferent and afferent fibers are arranged in a stereotyped pattern in the intermediate zone (IZ). Here, we studied the mechanism of axonal pathway formation by identifying a molecule that is expressed in a subset of cortical axons in the rat. We found that T-cadherin (T-cad), a member of the cadherin family, is expressed in deep-layer cell axons projecting to subcortical structures, but not in upper layer callosal axons projecting to the contralateral cortex. Ectopic expression of T-cad in upper layer cells induced axons to project toward subcortical structures via the upper part of the IZ. Moreover, the axons of deep-layer cells in which T-cad expression was suppressed by RNAi projected towards the contralateral cortex via an aberrant route. These results suggest that T-cad is involved in axonal pathway formation in the developing cortex.