Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparison of SNP Variation and Distribution in Indigenous Ethiopian and Korean Cattle (Hanwoo) Populations

Although a large number of single nucleotide polymorphisms (SNPs) have been identified from the bovine genome-sequencing project, few of these have been validated at large in Bos indicus breeds. We have genotyped 192 animals, representing 5 cattle populations of Ethiopia, with the Illumina Bovine 8K SNP BeadChip. These include 1 Sanga (Danakil), 3 zebu (Borana, Arsi and Ambo), and 1 zebu × Sanga intermediate (Horro) breeds. The Hanwoo (Bos taurus) was included for comparison purposes. Analysis of 7,045 SNP markers revealed that the mean minor allele frequency (MAF) was 0.23, 0.22, 0.21, 0.21, 0.23, and 0.29 for Ambo, Arsi, Borana, Danakil, Horro, and Hanwoo, respectively. Significant differences of MAF were observed between the indigenous Ethiopian cattle populations and Hanwoo breed (p < 0.001). Across the Ethiopian cattle populations, a common variant MAF (≥0.10 and ≤0.5) accounted for an overall estimated 73.79% of the 7,045 SNPs. The Hanwoo displayed a higher proportion of common variant SNPs (90%). Investigation within Ethiopian cattle populations showed that on average, 16.64% of the markers were monomorphic, but in the Hanwoo breed, only 6% of the markers were monomorphic. Across the sampled Ethiopian cattle populations, the mean observed and expected heterozygosities were 0.314 and 0.313, respectively. The level of SNP variation identified in this particular study highlights that these markers can be potentially used for genetic studies in African cattle breeds.
Identification of Signaling Pathways Mediating Cell Cycle Arrest and Apoptosis Induced by Porphyromonas gingivalis in Human Trophoblasts

ABSTRACT Epidemiological and interventional studies of humans have revealed a close association between periodontal diseases and preterm delivery of low-birth-weight infants. Porphyromonas gingivalis, a periodontal pathogen, can translocate to gestational tissues following oral-hematogenous spread. We previously reported that P. gingivalis invades extravillous trophoblast cells (HTR-8) derived from the human placenta and inhibits proliferation through induction of arrest in the G1 phase of the cell cycle. The purpose of the present study was to identify signaling pathways mediating cellular impairment caused by P. gingivalis. Following P. gingivalis infection, the expression of Fas was induced and p53 accumulated, responses consistent with response to DNA damage. Ataxia telangiectasia- and Rad3-related kinase (ATR), an essential regulator of DNA damage checkpoints, was shown to be activated together with its downstream signaling molecule Chk2, while the p53 degradation-related protein MDM2 was not induced. The inhibition of ATR prevented both G1 arrest and apoptosis caused by P. gingivalis in HTR-8 cells. In addition, small interfering RNA (siRNA) knockdown of p53 abrogated both G1 arrest and apoptosis. The regulation of apoptosis was associated with Ets1 activation. HTR-8 cells infected with P. gingivalis exhibited activation of Ets1, and knockdown of Ets1 with siRNA diminished both G1 arrest and apoptosis. These results suggest that P. gingivalis activates cellular DNA damage signaling pathways that lead to G1 arrest and apoptosis in trophoblasts.
The costs of a big brain: extreme encephalization results in higher energetic demand and reduced hypoxia tolerance in weakly electric African fishes

A large brain can offer several cognitive advantages. However, brain tissue has an especially high metabolic rate. Thus, evolving an enlarged brain requires either a decrease in other energetic requirements, or an increase in overall energy consumption. Previous studies have found conflicting evidence for these hypotheses, leaving the metabolic costs and constraints in the evolution of increased encephalization unclear. Mormyrid electric fishes have extreme encephalization comparable to that of primates. Here, we show that brain size varies widely among mormyrid species, and that there is little evidence for a trade-off with organ size, but instead a correlation between brain size and resting oxygen consumption rate. Additionally, we show that increased brain size correlates with decreased hypoxia tolerance. Our data thus provide a non-mammalian example of extreme encephalization that is accommodated by an increase in overall energy consumption. Previous studies have found energetic trade-offs with variation in brain size in taxa that have not experienced extreme encephalization comparable with that of primates and mormyrids. Therefore, we suggest that energetic trade-offs can only explain the evolution of moderate increases in brain size, and that the energetic requirements of extreme encephalization may necessitate increased overall energy investment.
BRVST: Efficient and Content-Expressive Information Matching Overlay in Wireless Networks

Efficient and flexible information matching over wireless networks has become increasingly important and challenging with the popularity of smart devices and the growth of social-network-based applications. Some existing approaches designed for wired networks are not applicable to wireless networks, due to their overwhelming control overheads. In this paper, we propose a reliable and scalable binary range vector summary tree (BRVST) infrastructure for flexible information expression support, effective content matching and timely information dissemination over the dynamic wireless network. A novel attribute range vector structure has been introduced for efficient and accurate content representation and a summary tree structure to facilitate information aggregation. For robust and scalable operations over dynamic wireless network, the proposed overlay system exploits a virtual hierarchical geographic management framework. Extensive simulations demonstrate that BRVST has a significantly faster event matching speed, while incurs very low storage and traffic overhead, as compared with peer schemes tested.
Nutrition During Pregnancy and the Effect of Carbohydrates on the Offspring’s Metabolic Profile: In Search of the “Perfect Maternal Diet”

Fetal growth and development is primarily dependent upon the nutritional, hormonal and metabolic environment provided by the mother. A wartime famine study in Holland first showed that a low food intake reduces the glucose offered to the fetus and thus produces smaller size infants at birth. Maternal glucose regulation is however affected by numerous factors including physiological changes of pregnancy (e.g. insulin resistance [IR]), pathological conditions (e.g. gestational diabetes mellitus) and maternal nutrition. Maternal glucose is substantially influenced by the type of carbohydrates in the diet through its direct effect on glycemia. The rate at which each carbohydrate raises blood glucose levels after ingestion, can be measured via the dietary glycemic index (GI). Carbohydrate type and the GI of the diet enhance or inhibit abnormal hyperglycemia during pregnancy caused by either pathological conditions or the inability of the mother to cope with the physiological IR of pregnancy. In turn, maternal gestational hyperglycemia may be involved in the pathogenesis of IR, impaired glucose tolerance, type 2 diabetes mellitus, the Metabolic Syndrome and subsequent cardiovascular diseases in adult offspring. A low GI maternal diet has been associated with measurable benefits to the offspring. These include a positive effect on altering maternal blood glucose production, insulinemia and reduced adiposity as well as fetal and placental insulin and glucose regulation, fetal growth, birth weight and offspring adiposity. We review the possible links between dietary carbohydrate in health during pregnancy and the effect of maternal carbohydrate ingestion on programming the offspring’s metabolic profile.
The role of BH3-only protein Bim extends beyond inhibiting Bcl-2–like prosurvival proteins

Proteins of the Bcl-2 family are critical regulators of apoptosis, but how its BH3-only members activate the essential effectors Bax and Bak remains controversial. The indirect activation model suggests that they simply must neutralize all of the prosurvival Bcl-2 family members, whereas the direct activation model proposes that Bim and Bid must activate Bax and Bak directly. As numerous in vitro studies have not resolved this issue, we have investigated Bim's activity in vivo by a genetic approach. Because the BH3 domain determines binding specificity for Bcl-2 relatives, we generated mice having the Bim BH3 domain replaced by that of Bad, Noxa, or Puma. The mutants bound the expected subsets of prosurvival relatives but lost interaction with Bax. Analysis of the mice showed that Bim's proapoptotic activity is not solely caused by its ability to engage its prosurvival relatives or solely to its binding to Bax. Thus, initiation of apoptosis in vivo appears to require features of both models.
Radiation therapy for liver metastases

Purpose of reviewThe liver is a common site of metastatic disease. Systemic therapy is most frequently the preferred therapy for patients with liver metastases, but surgical excision or tumor ablation strategies are often considered for patients with limited disease and favorable histology. Advances in radiation therapy technology made it possible to deliver potent biological doses to limited volumes of the liver with high precision in a few fractions. This method is known as stereotactic body radiation therapy (SBRT). Low-dose radiation therapy administered to the whole-liver radiation therapy (WLRT) is not regularly used for palliation of patients with massive liver metastases. The purpose of this review is to present an update of the most recent literature on SBRT and WLRT. Recent findingsRecently published studies confirm the role of SBRT as a highly effective treatment for ablation of liver metastases. The toxicity related to the therapy is mild or moderate. This treatment is indicated for patients with limited burden of intrahepatic and extrahepatic disease. Low-dose WLRT is a useful treatment for symptom palliation in patients with end-stage cancer and diffuse metastatic infiltration of the liver which became refractory to systemic treatment. SummarySBRT and WLRT are highly efficient in the treatment of patients with liver metastases. However, prospective randomized trials in radiation therapy for liver metastases are warranted.
Mitochondrial electron transport chain complexes, catalase and markers of oxidative stress in platelets of patients with severe aluminum phosphide poisoning

Aluminum phosphide (ALP), a widely used fumigant and rodenticide, leads to high mortality if ingested. Its toxicity is due to phosphine that is liberated when it comes in contact with moisture. The exact site or mechanism of action of phosphine is not known, although it is widely believed that it affects mitochondrial oxidative phosphorylation. Basic serum biochemical parameters, activity of mitochondrial complexes, antioxidant enzymes and parameters of oxidative stress were estimated in the platelets of 21 patients who developed severe poisoning following ALP ingestion. These parameters were compared with 32 healthy controls and with 22 patients with shock due to other causes (cardiogenic shock (11), septic shock (9) and hemorrhagic shock (2)). The serum levels of creatine kinase-muscle brain and lactate dehydrogenase were higher in patients poisoned with ALP, whereas a significant decrease was observed in the activities of mitochondrial complexes I, II and IV. The activity of catalase was lower but the activities of superoxide dismutase and glutathione peroxidase were unaffected in them. A significant increase in lipid peroxidation and protein carbonylation was observed, whereas total blood thiol levels were lower. In patients severely poisoned with ALP, not only cytochrome c oxidase but also other complexes are involved in mitochondrial electron transport, and enzymes are also inhibited.
A Toolkit for User-Level File Systems

This paper describes a C++ toolkit for easily extending the Unix file system. The toolkit exposes the NFS interface, allowing new file systems to be implemented portably at user level. A number of programs have implemented portable, user-level file systems. However, they have been plagued by low-performance, deadlock, restrictions on file system structure, and the need to reboot after software errors. The toolkit makes it easy to avoid the vast majority of these problems. Moreover, the toolkit also supports user-level access to existing file sys tems through the NFS interface—a heretofore rarely employed technique. NFS gives software an asynchronous, low-level interface to the file system that can greatly benefit the performance, security, and scalability of certain applications. The toolkit uses a new asynchronous I/O library that makes it tractable to build large, event-drive n programs that never block.
Rostral and caudal prefrontal contribution to creativity: a meta-analysis of functional imaging data

Creativity is of central importance for human civilization, yet its neurocognitive bases are poorly understood. The aim of the present study was to integrate existing functional imaging data by using the meta-analysis approach. We reviewed 34 functional imaging studies that reported activation foci during tasks assumed to engage creative thinking in healthy adults. A coordinate-based meta-analysis using Activation Likelihood Estimation (ALE) first showed a set of predominantly left-hemispheric regions shared by the various creativity tasks examined. These regions included the caudal lateral prefrontal cortex (PFC), the medial and lateral rostral PFC, and the inferior parietal and posterior temporal cortices. Further analyses showed that tasks involving the combination of remote information (combination tasks) activated more anterior areas of the lateral PFC than tasks involving the free generation of unusual responses (unusual generation tasks), although both types of tasks shared caudal prefrontal areas. In addition, verbal and non-verbal tasks involved the same regions in the left caudal prefrontal, temporal, and parietal areas, but also distinct domain-oriented areas. Taken together, these findings suggest that several frontal and parieto-temporal regions may support cognitive processes shared by diverse creativity tasks, and that some regions may be specialized for distinct types of processes. In particular, the lateral PFC appeared to be organized along a rostro-caudal axis, with rostral regions involved in combining ideas creatively and more posterior regions involved in freely generating novel ideas.
Physiological Parameters Measurement Based on Wheelchair Embedded Sensors and Advanced Signal Processing

This paper presents a multisensing system with wireless communication capabilities embedded on a smart wheelchair that can measure physiological parameters such as heart rate and respiratory rate in an unobtrusive way. Ballistocardiography (BCG) sensors and a three-axis inertial microelectromechanical system accelerometer are embedded on the seat or in the backrest of the wheelchair and the acquired data are transmitted by Wi-Fi to a laptop computer for advanced data processing and logging. In addition, a 3-D accelerometer with ZigBee communication capability is used to extract information about the user's posture. Considering the static and dynamic use of the wheelchair, an extended set of measurements for different utilization scenarios was analyzed. An important part of this paper is focused on BCG noise and artifacts removal and heart rate and respiratory rate accurate estimation from BCG signal using wavelet-based filtering and independent component analysis algorithms. A study on wavelet-based filtering considering different types of mother wavelets and different levels of decomposition was also carried out. In the future, other signals will also be acquired to improve the system capabilities and flexibility.
The Communicative Activity of "Making Suggestions" as an Interactional Process: Towards a Dialog Model for HAI

Dialog modeling of making suggestions in human-agent interaction is a challenge due to the socially delicate nature of a suggestion and ensuing interactional negotiations. A basic first dialog model for making suggestions was tested in the context of schedule management assistance by an embodied conversational agent with elderly and mildly cognitively impaired persons. Analysis showed that users responded according to human social structures with most response types bearing potential challenges concerning the system's language understanding and the users' intention interpretation:next to explicit answers, users produced implicit versions for acceptance or resistance and further requests for information or modifications. Thus, an enhanced dialog model with a newly added clarification sequence and a new multi-conditional entry sequence was tested in a second study with the autonomous system. Initial observations show a promising performance of the dialog model.
Tectonic Exhumation and Climate Driven Erosion in Extensional Mountain Blocks: Two Examples from California, USA

Low-angle detachment fault systems are important elements of active plate boundaries, yet kinematic relationships between detachment faults and inception of transform plate margins are poorly understood. The west Salton detachment fault (WSDF) is a major low-angle normal fault that formed coeval with localization of the Pacific-North America plate boundary in Coachella Valley. Low-temperature thermochronometry (apatite U/Th-He; AHe; n=29 samples) and thermal history modeling of samples from the Santa Rosa Mountains (SRM) reveal that initial exhumation along the WSDF began at ca. 8 Ma, and is responsible for exhumation of the footwall from depths of ~3 – 4 km. The timing of extension initiation suggests that perturbation of relative plate motions at 8 Ma is responsible for initiation of the southern San Andreas system in the Salton Trough, in contrast with evidence for progressive localization of plate boundary strain in the Gulf of California. Detachment-related extension proceeded at moderate rates; vertical exhumation was 0.15 – 0.36 km/Ma, with maximum fault slip rates of ~1.2 – 3.0 km/Ma. An uplifted fossil helium partial retention zone is present in the eastern SRM, while a deeper crustal section has been exhumed along the Pleistocene high-angle Santa Rosa fault (SFR) in the southwest SRM. AHe isochrons across the SRM indicate post-WSDF vertical exhumation along the SRF was ~1.3 km/Ma. Pleistocene regional tectonic reorganization was contemporaneous
UvA-DARE ( Digital Academic Repository ) EuroGOV : Engineering a Multilingual Web Corpus

EuroGOV is a multilingual web corpus that was created to serve as the document collection for WebCLEF, the CLEF 2005 web retrieval task. EuroGOV is a collection of web pages crawled from the European Union portal, European Union member state governmental web sites, and Russian government web sites. The corpus contains over 3 million documents written in more than 20 different European languages. In this paper we provide a detailed description of the EuroGOV collection.
Discriminative sum types locate the source of type errors

We propose a type system for locating the source of type errors in an applied lambda calculus with ML-style polymorphism. The system is based on discriminative sum types---known from work on soft typing---with annotation subtyping and recursive types. This way, type clashes can be registered in the type for later reporting. The annotations track the potential producers and consumers for each value so that clashes can be traced to their cause.Every term is typeable in our system and type inference is decidable. A type derivation in our system describes all type errors present in the program, so that a principal derivation yields a principal description of all type errors present. Error messages are derived from completed type derivations. Thus, error messages are independent of the particular algorithm used for type inference, provided it constructs such a derivation.
Heat Shock Transcription Factor Hsf1 Is Involved in Tumor Progression via Regulation of Hypoxia-Inducible Factor 1 and RNA-Binding Protein HuR

ABSTRACT Previously we demonstrated that the heat shock transcription factor Hsf1 is indispensable for transformation of mammary epithelial cells by the Her2 oncogene. Since Hsf1 affects oncogene-induced senescence (OIS), these findings suggest that Hsf1 affects tumor initiation when OIS plays a role. Indeed, here we report that Hsf1 knockout suppressed mammary hyperplasia in Her2-expressing mice and reduced tumor emergence. On the other hand, Hsf1 expression increases with advanced breast cancer, indicating that there is an additional role of Hsf1 in tumor progression. We studied rare tumors that developed in Hsf1-knockout mice and found that these tumors grew slower than tumors in control animals and showed suppressed angiogenesis. Similarly, in the xenograft model, knockdown of Hsf1 suppressed angiogenesis, which was associated with suppression of the HIF-1 pathway. Suppression of HIF-1 was at the level of translation due to downregulation of the RNA-binding protein HuR. Importantly, besides HIF-1, HuR controls translation of other major regulators of cancer progression, many of which were suppressed in Hsf1-knockdown cells. Therefore, in addition to OIS, Hsf1 regulates the HuR–HIF-1 pathway, thus affecting both cancer initiation and progression.
Demographic Characteristics of the Population of the United States 1930-1950: County-Level [MRDF]

This dataset contains [U.S.] county-level data for total population and net migration by age sex and color.The data are available for total population Negroes and other races. For 1930 and 1940 the population is tabulated in five-year intervals until age thirty-four and in ten-year intervals thereafter. For 1950 the numbers of whites and non-whites are given by sex and age in five-year intervals. There are a total of 3111 counties including a few aggregated spatial units to accommodate mergers and divisions. Extensive error checks were performed on the data by the original researchers. There are approximately 180000 card-image equivalents. (EXCERPT)