Miracle-dz/UniFAR-FTUs huggingface dataset:
Protein networks identify novel symbiogenetic genes resulting from plastid endosymbiosis

Significance Endosymbiotic gene transfer from the plastid genome to the nucleus comprises the most significant source of horizontal gene transfer in photosynthetic eukaryotes. We investigated genomic data at the infragenic level to determine whether the cyanobacterial endosymbiont also contributed gene fragments (i.e., domains) to create novel nuclear-encoded proteins. We found 67 such gene families that are expressed as RNA and widely distributed among plants and algae. At least 23 genes are putatively involved in redox regulation and light response, namely the maintenance of a photodynamic organelle. Our results add a new layer of complexity to plastid integration and point to the role of fused proteins as key players in this process. The integration of foreign genetic information is central to the evolution of eukaryotes, as has been demonstrated for the origin of the Calvin cycle and of the heme and carotenoid biosynthesis pathways in algae and plants. For photosynthetic lineages, this coordination involved three genomes of divergent phylogenetic origins (the nucleus, plastid, and mitochondrion). Major hurdles overcome by the ancestor of these lineages were harnessing the oxygen-evolving organelle, optimizing the use of light, and stabilizing the partnership between the plastid endosymbiont and host through retargeting of proteins to the nascent organelle. Here we used protein similarity networks that can disentangle reticulate gene histories to explore how these significant challenges were met. We discovered a previously hidden component of algal and plant nuclear genomes that originated from the plastid endosymbiont: symbiogenetic genes (S genes). These composite proteins, exclusive to photosynthetic eukaryotes, encode a cyanobacterium-derived domain fused to one of cyanobacterial or another prokaryotic origin and have emerged multiple, independent times during evolution. Transcriptome data demonstrate the existence and expression of S genes across a wide swath of algae and plants, and functional data indicate their involvement in tolerance to oxidative stress, phototropism, and adaptation to nitrogen limitation. Our research demonstrates the “recycling” of genetic information by photosynthetic eukaryotes to generate novel composite genes, many of which function in plastid maintenance.
Frontal and temporal lobe contributions to emotional enhancement of memory in behavioral-variant frontotemporal dementia and Alzheimer's disease

Emotional events gain special priority in how they are remembered, with emotionally arousing events typically recalled more vividly and with greater confidence than non-emotional events. In dementia, memory and emotion processing are affected to varying degrees, however, whether emotional enhancement of memory for complex ecologically-valid events is differentially affected across dementia syndromes remains unclear, with previous studies examining effects of emotion on simple visual recognition only. Here, we examined memory for an emotionally arousing short story and a closely matched, emotionally neutral story in behavioral-variant frontotemporal dementia (bvFTD) (n = 13) and Alzheimer's disease (AD) (n = 14), and contrasted their performance with healthy controls (n = 12). Multiple-choice recognition memory for specific details of the story was assessed after a 1-h delay. While AD and control groups showed enhanced memory for the emotional story, the bvFTD group recalled a similar number of details from the emotional and neutral stories. Voxel-based morphometry analyses revealed emotional enhancement of memory correlated with distinct brain regions in each patient group. In AD, emotional enhancement was associated with integrity of the bilateral hippocampus, parahippocampal gyri, temporal fusiform gyrus and frontal pole, regions typically implicated in memory processes. In contrast in bvFTD, integrity of emotion processing regions, including the orbitofrontal cortex, right amygdala and right insula, correlated with the extent emotion enhanced memory. Our results reveal that integrity of frontal and temporal regions determine the quality and nature of emotional memories. While emotional enhancement of memory is present in mild AD, in bvFTD emotion does not facilitate memory retrieval for complex realistic events. This attenuation of emotional enhancement is due to degradation of emotion processing regions, which may be important for modulating levels of arousal in response to emotional events in these patients.
Example-Based Automatic Font Generation

It is difficult and time-consuming to create and maintain a consistent style in all characters in manual font design process. Thus, we present a method for automatically generating a new font from a userdefined example. From each character outline, a skeleton is derived to be used as a topological structure. The system can then represent an arbitrary font using a weighted blend of outlines and skeletons from template fonts. The system takes the outline of a single character drawn by the user and computes blending weights from a database to reproduce the given outline. The weights are then applied to all characters to synthesize the new font. In this paper, the algorithm is described in detail and its quality evaluated with some examples.
Measuring Corporate Social Performance: A Review

This paper reviews the literature on corporate social performance (CSP) measurement and sets that literature into a theoretical context. Following a review of CSP theory development and the literature on relationships between CSP and corporate financial performance, Wood's CSP model (Wood, D.J. (1991). Corporate social performance revisited. Academy of Management Review, 16, pp. 691–718) is used as an organizing device to present and discuss studies that use particular measures of CSP. Conclusions emphasize the need for CSP scholars to refocus on stakeholders and society, and to incorporate relevant literatures from other scholarly domains.
Congenital urogenital abnormalities in children with congenital hypothyroidism

Background: Congenital hypothyroidism (CH), as one of the most common congenital endocrine disorders, may be significantly associated with congenital malformations. This study investigates urogenital abnormalities in children with primary CH (PCH). Methods: This case-control study was conducted on 200 children aged three months to 1 year, referred to Amir-Kabir Hospital, Arak, Iran. One hundred children with PCH, as the case group, and 100 healthy children, as the control group, were selected using convenient sampling. For all children, demographic data checklists were filled, and physical examination, abdomen and pelvic ultrasound and other diagnostic measures (if necessary) were performed to evaluate the congenital urogenital abnormalities including anomalies of the penis and urethra, and disorders and anomalies of the scrotal contents. Results: Among 92 (100%) urogenital anomalies diagnosed, highest frequencies with 37 (40.2%), 26(28.2%) and 9 (9.7%) cases including hypospadias, Cryptorchidism, and hydrocele, respectively. The frequency of urogenital abnormalities among 32 children with PCH, with 52 cases (56.5%) was significantly higher than the frequency of abnormalities among the 21 children in the control group, with 40 cases (43.4%). (OR=2.04; 95%CI: 1.1-3.6; p=0.014). Conclusion: Our study demonstrated that PCH is significantly associated with the congenital urogenital abnormalities. However, due to the lack of evidence in this area, further studies are recommended to determine the necessity of conducting screening programs for abnormalities of the urogenital system in children with CH at birth.
Minimalist open-page: A DRAM page-mode scheduling policy for the many-core era

Contemporary DRAM systems have maintained impressive scaling by managing a careful balance between performance, power, and storage density. In achieving these goals, a significant sacrifice has been made in DRAM's operational complexity. To realize good performance, systems must properly manage the significant number of structural and timing restrictions of the DRAM devices. DRAM's use is further complicated in many-core systems where the memory interface is shared among multiple cores/threads competing for memory bandwidth.
Prebiotics and Bioactive Milk Fractions Affect Gut Development, Microbiota, and Neurotransmitter Expression in Piglets

Objective: This study tested the hypothesis that the addition of prebiotics and 2 functional milk ingredients to infant formula would maintain normal growth and gut development, and modify microbiota composition and neurotransmitter gene expression in neonatal piglets. Methods: Two-day-old male piglets (n = 24) were fed formula (CONT) or formula with polydextrose (1.2 g/100 g diet), galactooligosaccharides (3.5 g/100 g diet), bovine lactoferrin (0.3 g/100 g diet), and milk fat globule membrane-10 (2.5 g/100 g diet) (TEST) for 30 days. On study day 31, intestinal samples, ileal and colonic contents, and feces were collected. Intestinal histomorphology, disaccharidase activity, serotonin (5’HT), vasoactive intestinal peptide (VIP), and tyrosine hydroxylase (TH) were measured. Gut microbiota composition was assessed by pyrosequencing of the V3–V5 regions of 16S rRNA and quantitative polymerase chain reaction. Results: Body weight of piglets on TEST was greater (P ⩽ 0.05) than CONT on days 17 to 30. Both groups displayed growth patterns within the range observed for sow-reared pigs. TEST piglets had greater jejunal lactase (P = 0.03) and higher (P = 0.003) ileal VIP expression. TEST piglets tended to have greater (P = 0.09) sucrase activity, longer (P = 0.08) ileal villi, and greater (P = 0.06) duodenal TH expression. Microbial communities of TEST piglets differed from CONT in ascending colon (AC, P = 0.001) and feces (P ⩽ 0.05). CONT piglets had greater relative abundances of Mogibacterium, Collinsella, Klebsiella, Escherichia/Shigella, Eubacterium, and Roseburia compared with TEST piglets in AC. In feces, CONT piglets harbored lower (P ⩽ 0.05) proportions of Parabacteroides, Clostridium IV, Lutispora, and Sutterella than TEST piglets. Conclusions: A mixture of bioactive ingredients improved weight gain and gut maturation, modulated colonic and fecal microbial composition, and reduced the proportions of opportunistic pathogens.
Assistive technologies for the disabled and for the new generation of senior citizens: the e-Tools architecture

In this paper we present our exploratory ideas about the integration of agent technology with other technologies to build specific e-tools for the disabled and for the new generation of senior citizens. “e-Tools” stands for Embedded Tools, as we aim to embed intelligent assistive devices in homes and other facilities, creating ambient intelligence environments to give support to patients and caregivers. In particular, we aim to explore the benefits of the concept of situated intelligence to build artefacts that will enhance the autonomy of the target user group in their daily life.
Security of classical noise-based cryptography

We examine the security of a protocol on cryptographic key distribution proposed by Yuen and Kim (Yuen H P and Kim A M 1998 Phys. Lett. A 241 135). Theoretical and experimental analysis shows that, even if the eavesdropper can receive more photons than the legitimate receiver, secure key distribution is possible as long as the signal-to-noise ratio of the eavesdropper does not exceed eight times (9 dB) that of the receiver. Secure key distribution was demonstrated using conventional fibre optics. The secure key transmission rate in the experiment was estimated to be 2 Mb s-1 at its maximum (0.04 bit per sender's bit). The present protocol has advantages over other quantum key distribution protocols in that it is more efficient and more easily implemented, but careful design and management are necessary to ensure the security of the cryptosystem.
Direct binding of Lef1 to sites in the boz promoter may mediate pre–midblastula‐transition activation of boz expression

The Nieuwkoop center provides signals essential for the establishment of the dorsal gastrula organizer in vertebrates. Activation of β‐catenin is one of the events in the Nieuwkoop center that lead to activation of dorsal‐specific genes during blastula and early gastrula stages. Zebrafish bozozok (boz) mutant embryos have severe defects in axial mesoderm and anterior neuroectoderm. The boz gene is activated in the organizer in response to β‐catenin signaling, and Boz protein has been demonstrated to contribute to organizer formation by repression of ventralizing genes, including bmp2b, vega1, and vega2. Here, we investigate the timing and molecular mechanism by which boz expression is activated in the organizer. We demonstrate that boz is already expressed before midblastula transition (MBT). We further identify high‐affinity binding sites for Tcf/Lef1 within the boz promoter region. These sites, together with the finding that β‐catenin induces boz expression, indicate that transcription of boz may be activated directly by β‐catenin/Lef1. We hypothesize that pre‐MBT activation of boz may be important to build up a sufficiently strong antagonizing activity against zygotic ventralizing genes activated immediately post‐MBT. Thus, the early onset of boz expression may be crucial for organizer establishment in the presence of ubiquitous maternal activators of ventralizing genes. Developmental Dynamics, 2003. © 2003 Wiley‐Liss, Inc.
Decaf: Moving Device Drivers to a Modern Language

Writing code to interact with external devices is inherently difficult, and the added demands of writing device drivers in C for kernel mode compounds the problem. This environment is complex and brittle, leading to increased development costs and, in many cases, unreliable code. Previous solutions to this problem ignore the cost of migrating drivers to a better programming environment and require writing new drivers from scratch or even adopting a new operating system. We present Decaf Drivers, a system for incrementally converting existing Linux kernel drivers to Java programs in user mode. With support from program-analysis tools, Decaf separates out performance-sensitive code and generates a customized kernel interface that allows the remaining code to be moved to Java. With this interface, a programmer can incrementally convert driver code in C to a Java decaf driver. The Decaf Drivers system achieves performance close to native kernel drivers and requires almost no changes to the Linux kernel. Thus, Decaf Drivers enables driver programming to advance into the era of modern programming languages without requiring a complete rewrite of operating systems or drivers. With five drivers converted to Java, we show that Decaf Drivers can (1) move the majority of a driver's code out of the kernel, (2) reduce the amount of driver code, (3) detect broken error handling at compile time with exceptions, (4) gracefully evolve as driver and kernel code and data structures change, and (5) perform within one percent of native kernel-only drivers.
A combined natural supplement lowers LDL cholesterol in subjects with moderate untreated hypercholesterolemia: a randomized placebo-controlled trial

Abstract Objective: To investigate the effect of a natural cholesterol-lowering supplement (NCLS) containing red yeast rice, policosanols and artichoke leaf extracts on blood lipid concentrations as well as on safety parameters when given over 16 weeks in 100 volunteers with untreated moderate hypercholesterolemia, in a randomized, double-blind, placebo-controlled trial. Results: Reduction of primary outcome low-density lipoprotein cholesterol [−0.22 g/L (95% confidence interval, CI: −0.31 to −0.12) corresponding to −14.3% from baseline (95% CI: −21.5 to −7.2) compared to placebo], as well as total cholesterol, apolipoprotein B100 and apolipoprotein B100/apolipoprotein A-I ratio, were observed after 16 weeks of supplementation with NCLS. These effects were already observed at Week 4 and 10 of supplementation. No significant changes were observed in high-density lipoprotein, triacylglycerol, creatine kinase, lactate dehydrogenase and coenzyme Q10 levels, as well as in markers of liver and renal function. Conclusions: The NCLS was effective in reducing low-density lipoprotein cholesterol and apolipoprotein B100 in subjects with moderate hypercholesterolemia, without modifying safety parameters.
Need for cognition and interpersonal influence : Individual differences in impact on dyadic decisions

The role of need for cognition (NC; J. T Cacioppo & R. E. Petty, 1982) in dyadic decisions was investigated. Consistent with the notion that individual differences in NC correspond to differences in attitude strength, the prediscussion views of people high in NC were found to be more predictive of dyadic decisions than were the prediscussion views of people low in NC. High-NC people were viewed by their discussion partners (and by themselves) as being more effective persuaders, generating more arguments to support their views (and thus counter those of their partners), and generating more valid arguments than their low-NC counterparts. The role of individual differences in understanding asymmetries in group member influence and in predicting collective decision outcomes is discussed.
Neuroendocrine Asymmetry

The information available at present clearly indicates that asymmetry exists from the level of elementary particles to the human cerebral cortex, the latest stage of evolution. Cerebral lateralization is one of the well-known asymmetries. This paper summarizes the data published in the past decades on the asymmetry of the neuroendocrine system. The information on the sided-differences between the gonads, adrenals, and thyroid lobes and that on the lateralization of hypothalamic, limbic, and other brain structures participating in the control of the endocrine glands as well as relevant clinical observations are reviewed here. The innervation of the peripheral endocrine glands is also briefly summarized because the afferent and efferent fibers of these glands may represent one part of the pathway involved in neuroendocrine asymmetry. The data reviewed clearly indicate that some kind of asymmetry (morphological, biochemical, physiological, pathological) is evident at different levels of the neuroendocrine system (at limbic, hypothalamic, peripheral endocrine glands and their innervation) and there are species, sex, and age differences. Most of the information accumulated deals with the CNS-gonadal system. A majority of the observations suggest that in both male and female rats there is a predominance of the right half of brain structures controlling gonadal function. The asymmetry, however, is not restricted to CNS structures: it also exists at the level of the gonads, including their innervation. It appears that the characteristic pattern of the CNS-gonadal system becomes fixed only after sexual maturation. Very few reports are available suggesting some kind of asymmetry of the CNS-adrenal cortex and the CNS-thyroid system. There are convincing findings consistent with the view that in addition to the hypothalamo-adenohypophyseal system acting via the general circulation on the peripheral endocrine glands, there is also a pure neural link between the CNS and the gonads, the CNS and the adrenal gland, and also between the CNS and the thyroid. This link contains afferent and efferent pathways and is able to modulate the functional activity or the responsiveness of the gland. It may also serve as a neural reflex arc. It is assumed that the neuroendocrine asymmetry expresses itself through (i) hypophysiotrophic neurohormones and hormones of the peripheral endocrine glands, (ii) neural pathways, or (iii) a combination of (i) and (ii). The authors hope that this publication, in addition to providing an overview, will also stimulate research, both basic and clinical, in this exciting area of neuroendocrinology.
Loss of Reelin protects against atherosclerosis by reducing leukocyte–endothelial cell adhesion and lesion macrophage accumulation

Reelin in the circulation promotes vascular inflammation and atherosclerosis. Reelin in leukocytes for atherosclerosis The secreted protein Reelin has important functions in the central nervous system and in the vascular system. Receptors for Reelin are found on the endothelial cells that line blood vessels, prompting Ding et al. to investigate if Reelin contributed to atherosclerosis. Mice globally deficient in Reelin or lacking Reelin produced by the liver were protected from diet-induced atherosclerosis. Reelin deficiency prevented leukocytes from adhering to endothelial cells, a critical first step in the inflammatory response that promotes atherosclerosis. Blocking this activity of Reelin on endothelial cells may prevent atherosclerosis or complement existing strategies. The multimodular glycoprotein Reelin controls neuronal migration and synaptic transmission by binding to apolipoprotein E receptor 2 (Apoer2) and very low density lipoprotein receptor (Vldlr) on neurons. In the periphery, Reelin is produced by the liver, circulates in blood, and promotes thrombosis and hemostasis. To investigate if Reelin influences atherogenesis, we studied atherosclerosis-prone low-density lipoprotein receptor–deficient (Ldlr−/−) mice in which we inducibly deleted Reelin either ubiquitously or only in the liver, thus preventing the production of circulating Reelin. In both types of Reelin-deficient mice, atherosclerosis progression was markedly attenuated, and macrophage content and endothelial cell staining for vascular cell adhesion molecule–1 (VCAM-1) and intercellular adhesion molecule–1 (ICAM-1) were reduced at the sites of atherosclerotic lesions. Intravital microscopy revealed decreased leukocyte-endothelial adhesion in the Reelin-deficient mice. In cultured human endothelial cells, Reelin enhanced monocyte adhesion and increased ICAM1, VCAM1, and E-selectin expression by suppressing endothelial nitric oxide synthase (eNOS) activity and increasing nuclear factor κB (NF-κB) activity in an Apoer2-dependent manner. These findings suggest that circulating Reelin promotes atherosclerosis by increasing vascular inflammation, and that reducing or inhibiting circulating Reelin may present a novel approach for the prevention of cardiovascular disease.