Miracle-dz/UniFAR-FTUs huggingface dataset:
A novel clonality assay based on transcriptional analysis of the active X chromosome

Abstract The clonal origin of malignancy and he‐matopoiesis is a principal tenet of modern biology and medicine. This paper describes a highly specific and sensitive assay for the detection of clonality in cells and cell lineages suitable for studies in a large proportion of females. The specific ligase chain and/ or ligase detection reactions (LCR/LDR) are utilized at a polymorphic glucose‐6‐phosphate dehydrogen‐ase (G‐6‐PD) locus for discrimination of the mRNA transcripts of the active X chromosome. This combination approach circumvents problems encountered with other currently used assays of clonality based either on peptide G‐6‐PD polymorphism or on DNA methylation differences between the active and inactive X chromosomes. The veracity of this assay was verified by analysis of 19 random healthy females as well as by the study of hemopoietic and nonhemopo‐ietic tissues from a patient with clonal hemopoiesis/ polycythemia vera. Furthermore, we demonstrate that the G‐6‐PD locus used in our clonal assay does not display marked differences in methylation between the active and the inactive X chromosomes.
Gastric cancer: Laboratory bench to clinic

Abstract Gastric cancer is the second most common cause of cancer‐related mortality worldwide and the 14th overall cause of death. Detection of disease usually occurs at an advanced stage and overall survival rates for gastric cancer are poor. Our current model for gastric cancer progression clearly maintains Helicobacter infection as the primary inducer of gastric metaplastic and neoplastic disease. Helicobacter pylori is a ubiquitous organism, infecting more than half the world’s population. It has been suggested that this infection directly contributes to the formation of gastric cancer in up to 80% of cases; however, gastric malignancy develops in only a subset (< 1%) of infected patients. Therefore, predisposition to Helicobacter‐associated gastric cancer is most likely multifactorial, including the interaction of bacterial, host and environmental components. Our understanding of how the organism interacts with the gastric mucosa and synergizes with dietary and other environmental factors to induce malignant mucosal changes is evolving. Indeed, H. pylori has direct effects on the gastric mucosa, but the major factor in disease progression appears to be a robust host Th1 immune response in the setting of a permissive environment. In combination, these factors predispose to the formation of atrophy, metaplasia and gastric cancer. Understanding the interaction of the bacterium with the host and the environment can potentially identify patients most at risk. Identifying potentially removable factors (in addition to H. pylori infection) in the acquisition and progression of neoplastic disease may provide targets for early intervention and prevention strategies.
Environmental Perceptions Related to Physical Activity in High- and Low-Risk Counties

To identify whether perceptions about the physical activity environment were related to the prevalence of sedentary lifestyle, residents from high-risk (n = 153) or low-risk (n = 100) counties were interviewed. County risk status was determined by the prevalence of cardiovascular mortality, overweight, and sedentary lifestyle. Key public officials in the same counties were also interviewed. Residents in the low-risk county were more likely to report having sidewalks in their community and that these sidewalks were safe and well lit than residents living in the high-risk counties. Low-risk county residents also reported more indoor recreation facilities being available than the residents in the high-risk counties. Residents supported allocating tax dollars toward improving sidewalks, lighting, and so on. Thus a more conducive environment for physical activity was found in the low-risk county. Improving physical environments and individual perceptions could help increase physical activity behavior.
Selective blockade of N-methyl-D-aspartate (NMDA)-induced convulsions by NMDA antagonists and putative glycine antagonists: relationship with phencyclidine-like behavioral effects.

Antagonism of N-methyl-D-aspartate (NMDA)-induced convulsions by a variety of drugs was compared with their ability to produce phencyclidine (PCP)-like behavioral effects (locomotion and falling) in mice. Convulsions produced by i.c. v. administration of NMDA were antagonized, at doses that did not block kainate- and quisqualate-induced convulsions, by competitive NMDA antagonists (e.g., CPP and CGS 19755), noncompetitive antagonists (e.g., PCP and MK-801) and also by some putative glycine antagonists (7-chlorokynurenic acid and HA-966). Only the competitive and the noncompetitive NMDA antagonists produced locomotion and falling, and their potencies to do so correlated (r = 0.92) with their relative potencies to antagonize NMDA-induced convulsions. However, the PCP-like behavioral effects produced by the competitive antagonists were of a lesser magnitude than those of the noncompetitive antagonists, and occurred at doses higher than those needed to block NMDA-induced convulsions. The putative glycine antagonists 7-chlorokynurenic acid and HA-966 selectively blocked NMDA-induced convulsions, without producing PCP-like behavioral effects. The extent to which compounds produce PCP-like behavioral effects might depend in part on the specific component of the NMDA receptor complex with which they interact: i.e., the NMDA receptor, the NMDA receptor-associated ion channel or the glycine-sensitive modulatory site.
A multi-robot cooperative system considering both task allocation and execution issues

Low-level issues related to task execution are often oversimplified or ignored in research works of multi-robot cooperation. In this paper, a multi-robot cooperative system considering both high-level task allocation issues and low-level task execution issues is proposed. Simulation results show that both task allocation and execution algorithms will affect the system performance, which indicates that it is more reasonable to consider them as an integrated problem rather than independent issues. Practical experiments further verify the applicability of the cooperative system proposed in this paper.
Genetics, environment and bovine respiratory disease

Abstract The heritability estimates for resistance and/or susceptibility to bovine respiratory disease (BRD) are small, suggesting response to direct selection will be slow. The number of mammalian genetic markers associated with resistance to specific pathogens or improved immunity is increasing and will provide additional information for developing selection criteria for producing animals with an innate resistance to BRD. Environmental and management factors play significant roles in the prevalence of BRD and must be considered in a holistic approach to reducing BRD. Although no single solution for preventing BRD is likely to be discovered in the immediate future, the long-term outlook appears very promising.
Apolipoprotein E epsilon 4 is associated with the presence and earlier onset of hemorrhage in cerebral amyloid angiopathy.

BACKGROUND AND PURPOSE Cerebral amyloid angiopathy is an important cause of intracerebral hemorrhage in the elderly. The epsilon 4 allele of the apolipoprotein E gene, recently established as a genetic risk for Alzheimer's disease, has also been suggested as a possible risk factor for cerebral amyloid angiopathy. We sought to determine whether this allele is specifically associated with hemorrhages related to amyloid angiopathy and whether it correlates with the age at which first amyloid angiopathy-related hemorrhage occurs. METHODS Forty-five consecutive patients presenting with lobar hemorrhage were prospectively classified according to clinical, radiological, and when available, pathological features and evaluated for apolipoprotein E genotype. They were compared with 1899 elderly patients from a population-based sample and with 18 consecutive patients with hemorrhages in deep regions typical of a hypertensive mechanism. RESULTS Patients with multiple hemorrhages confined to the lobar territory demonstrated a greater than twofold overrepresentation (P < .001) in frequency of the apolipoprotein E epsilon 4 allele compared with the population-based sample. Apolipoprotein E genotypes of patients with hemorrhages in deep territories resembled the population sample. Among patients with strictly lobar hemorrhages, carriers of the epsilon 4 allele had their first hemorrhage more than 5 years earlier than noncarriers (mean age at first hemorrhage, 73.4 +/- 8.0 versus 78.9 +/- 7.4 years; P = .033). These effects were independent of the accompanying presence of Alzheimer's disease. CONCLUSIONS The data support a specific role for apolipoprotein E epsilon 4 in accelerating the process that leads to amyloid angiopathy-related hemorrhage.
Symptom prevalence, intensity, and distress in patients with inoperable lung cancer in relation to time of death.

PURPOSE To examine symptom prevalence, intensity, and association with distress in patients with inoperable lung cancer (LC), using time to death as point of reference. PATIENTS AND METHODS A consecutive sample of 400 patients completed the European Organisation for Research and Treatment of Cancer Quality of Life Questionnaire C30 plus a 13-item LC-specific scale and the Thurstone Scale of Symptom Distress-Lung Cancer at six time points during the first year after diagnosis. Patients were divided into subgroups, using data from the time point closest to death (< 1; 1 to 2; > 2 to 3; > 3 to 6; > 6 to 12; and > 12 months before death) for analysis. RESULTS More than 50% of patients in all subgroups reported problems related to physical, role, and emotional functioning; fatigue; dyspnea; and cough. In general, functional levels were lower and symptoms higher in subgroups closer to death. Notably, clinically relevant differences were also found in role and social functioning and appetite loss between the two groups furthest from death. A consistent pattern was found among the six subgroups, with breathing, pain, and fatigue rated as the symptoms most associated with distress. CONCLUSION High prevalence of symptoms was found in all subgroups, with higher intensity in subgroups closer to death, indicating a need for prophylactic and proactive symptom management. Less concordance was found among symptom prevalence, intensity, and association with distress in subgroups further from death. Future studies should investigate longitudinal associations between symptoms with low intensity and high distress, and examine their clinical implications.
Effect of season and social environment on testis size and semen quality of the adult Landrace boar.

Eight adult Landrace boars were housed for 12 mo in one of two social environments. Socially nonrestricted boars were penned adjacent to and allowed minimal physical contact with ovariectomized gilts hormonally induced into estrus every 2 wk. Socially restricted boars were penned behind solid walls to eliminate visual and physical contact with other pigs. All animals were subjected to natural changes in daylength. Semen was collected weekly; gel-free volume, gel weight, sperm concentration and number per ejaculate, sperm motility (percent and type) and semen pH were determined. Total protein, citric acid contents and alkaline phosphatase activity were measured in seminal plasma. Testis length and width and various body temperature measurements were recorded monthly. Except for percent motile sperm and alkaline phosphatase activity, all semen characteristics varied (P less than .05) with month. The pattern of seasonal change in semen volume was modified by social environment (group X month, P less than .05). Sperm numbers were highest in winter and lowest in spring and summer. Ejaculate protein and citric acid contents were highest in fall and winter; decreases in spring were associated with moderate ambient temperatures and increases in daylength (r = -.80, P less than .05). Testicular length for socially nonrestricted boars was maximum in November through January and minimum in April through July, and did not vary as extensively for socially restricted boars. Scrotal temperature was elevated during periods of high ambient temperature, but not to values detrimental to spermatogenic function. (ABSTRACT TRUNCATED AT 250 WORDS)
Zic1 promotes the expansion of dorsal neural progenitors in spinal cord by inhibiting neuronal differentiation.

The role of Zic1 was investigated by altering its expression status in developing spinal cords. Zic genes encode zinc finger proteins homologous to Drosophila Odd-paired. In vertebrate neural development, they are generally expressed in the dorsal neural tube. Chick Zic1 was initially expressed evenly along the dorsoventral axis and its expression became increasingly restricted dorsally during the course of neurulation. The dorsal expression of Zic1 was regulated by Sonic hedgehog, BMP4, and BMP7, as revealed by their overexpressions in the spinal cord. When Zic1 was misexpressed on the ventral side of the chick spinal cord, neuronal differentiation was inhibited irrespective of the dorsoventral position. In addition, dorsoventral properties were not grossly affected as revealed by molecular markers. Concordantly, when Zic1 was overexpressed in the dorsal spinal cord in transgenic mice, we observed hypercellularity in the dorsal spinal cord. The transgene-expressing cells were increased in comparison to those of truncated mutant Zic1-bearing mice. Conversely, we observed a significant cell number reduction without loss of dorsal properties in the dorsal spinal cords of Zic1-deficient mice. Taken together, these findings suggest that Zic1 controls the expansion of neuronal precursors by inhibiting the progression of neuronal differentiation. Notch-mediated inhibition of neuronal differentiation is likely to act downstream of Zic genes since Notch1 is upregulated in Zic1-overexpressing spinal cords in both the mouse and the chick.
Fecal Calprotectin Testing

the results of a multicenter, retrospective cross-sectional study were reported. The study included 131 pediatric patients with CD who had experienced at least a 6-month clinical remission with anti-tumor necrosis factor (TNF) agents and simultaneously underwent ileocolonoscopy and FC tests during follow-up. The study was pursued to investigate if FC could serve as a surrogate marker in assessing mucosal healing (MH) in this population. MH was defined as the absence of any ulcer on ileocolonoscopy. Among the 131 patients, MH was discovered in 87 patients (66.7%). In patients with MH versus those
One Year of Enzyme Replacement Therapy Reduces Globotriaosylceramide Inclusions in Podocytes in Male Adult Patients with Fabry Disease

Fabry nephropathy is associated with progressive accumulation of globotriaosylceramide (GL3) in podocytes. Reducing this GL3 burden may reduce podocyte injury. Sensitive methods to quantify podocyte GL3 content may determine whether a given strategy can benefit podocytes in Fabry disease. We developed an unbiased electron microscopic stereological method to estimate the average volume of podocytes and their GL3 inclusions in 6 paired pre- and post-enzyme replacement therapy (ERT) biopsies from 5 men with Fabry disease. Podocyte GL3 content was regularly reduced (average 73%) after 11–12 months of ERT. This was not detectable using a semi-quantitative approach. Parallel to GL3 reduction, podocytes became remarkably smaller (average 63%). These reductions in podocyte GL3 content or size were not significantly correlated with changes in foot process width (FPW). However, FPW after ERT was significantly correlated with the magnitude of the decrease in podocyte GL3 content from baseline to 11–12 months of ERT. Also podocytes exocytosed GL3 inclusions, a phenomenon correlated with their reduction in their GL3 content. Demonstrable after11–12 months, reduction in podocyte GL3 content allows for early assessment of treatment efficacy and shorter clinical trials in Fabry disease.
Tiny Microbes, Big Yields: enhancing food crop production with biological solutions

Plant‐associated microbiomes have tremendous potential to improve plant resilience and yields in farming systems. There is increasing evidence that biological technologies that use microbes or their metabolites can enhance nutrient uptake and yield, control pests and mitigate plant stress responses. However, to fully realize the potential of microbial technology, their efficacy and consistency under the broad range of real‐world conditions need to be improved. While the optimization of microbial biofertilizers and biopesticides is advancing rapidly to enable use in various soils, crop varieties and environments, crop breeding programmes have yet to incorporate the selection of beneficial plant–microbe interactions to breed ‘microbe‐optimized plants’. Emerging efforts exploring microbiome engineering could lead to microbial consortia that are better suited to support plants. The combination of all three approaches could be integrated to achieve maximum benefits and significantly improved crop yields to address food security.
Dynamical Network Forensics Based on Immune Agent

Current network forensics systems are static and not real-time. In order to overcome the shortages, a dynamical network forensics model based on artificial immune theory and multi-agent theory, referred to as DNF, is introduced here. Comparing with traditional computer forensics methods, the new method provides the capacity that gathering real-time evidence dynamically as soon as network intrusions take place and saving the evidence in a safe way to prepare for the collection and analysis of the original evidence. In this paper, architecture of the model and the definitions of its components inspired by the immunity theory are given out. The experiment shows that it is able to insure the authenticity, integrality and validity of the digital evidence, and it is a new method for dynamic computer forensics.
Aortobifemoral bypass via Paramedian Incision and Retroperitoneal Approach for Aortoiliac Occlusive Disease

Abstract Introduction : Aorto-bifemoral graft bypass operation is performed in the surgical treatment of aortoiliac occlusive occlusive disease. The conventional standard technique used is the median laparotomy and transperitoneal approach. In this study we evaluated the outcome of aortobifemoral bypass operation via paramedian and retroperitoneal approach. Methods : 17 patients were operated upon for aortobiiliac occlusive disease from January 2008 through December 2011. Mean age of the patients was 61.8 ± 8.9 (47–78 years). All patients except for one were operated via left paramedian vertical 8 to 10 cm incision approximately 6 cm to the left or right of midline, extending from a few centimeters above the umbilicus to just above the symphysis pubis. The aortas were reached retroperitoneally through this incision. Results : There was one postoperative death secondary to pulmonary complications. No intraoperative or postoperative surgical complication had occured. All patients were discharged from the hospital on antiplatelet therapy. Graft patency was evaluated by means of physical examination on discharge. Upon the patients’ hospital discharge, primary graft patency was 100%. The ankle-brachial indices measured from both the right and left sides were 0.51 ± 0.10 preopera-tively and 0.99 ± 0.14 postoperatively (p < 0.001). Discussion : A lot of complications can be observed due to median laparotomy such as evisceration, incisional hernia, peritonitis, bride ileus. We believe that retroperitoneal approach for aorto-bifemoral graft bypass operation in the patients with bilateral iliac arterial occlusive disease is a well tolerated minimally invasive operation when compared to the conventional median laparotomy approach.
The utility of contemporary and historical estimates of dispersal in determining response to habitat fragmentation in a tropical forest‐dependent bird community

It is often assumed that species which exhibit a greater propensity for dispersal are less susceptible to the impacts of habitat fragmentation; however, a growing body of literature suggests that such generalizations should be carefully evaluated as not all species appear to be equally sensitive to fragmentation. In this issue of Molecular Ecology, Callens et al. (2011) take an innovative approach to compare contemporary estimates of dispersal from an extensive mark‐recapture and patch occupancy data set with historical estimates derived from multilocus population genetic models for seven sympatric forest‐dependent species in the Taita Hills, Africa. As has been observed for forest‐dependent species from the Amazon, populations of sedentary species were more strongly differentiated and clustered when compared to those of more dispersive taxa. The most intriguing result recovered though, was that the five species with similar historical estimates of gene flow (dispersal) differed substantially in their contemporary dispersal rates, suggesting that for some species the propensity for dispersal has decreased over time. As a consequence, the authors suggest that post‐fragmentation estimates of dispersal on their own may not be the best predictors of how habitat fragmentation could affect forest‐dependent animal communities. This work significantly advances our understanding of the dynamics of habitat fragmentation and makes a strong case for the need to integrate data on historical processes with contemporary data.
Defective Metabolic Signaling in Adenylate Kinase AK1 Gene Knock-out Hearts Compromises Post-ischemic Coronary Reflow*

Matching blood flow to myocardial energy demand is vital for heart performance and recovery following ischemia. The molecular mechanisms responsible for transduction of myocardial energetic signals into reactive vasodilatation are, however, elusive. Adenylate kinase, associated with AMP signaling, is a sensitive reporter of the cellular energy state, yet the contribution of this phosphotransfer system in coupling myocardial metabolism with coronary flow has not been explored. Here, knock out of the major adenylate kinase isoform, AK1, disrupted the synchrony between inorganic phosphate Pi turnover at ATP-consuming sites and γ-ATP exchange at ATP synthesis sites, as revealed by 18O-assisted 31P NMR. This reduced energetic signal communication in the post-ischemic heart. AK1 gene deletion blunted vascular adenylate kinase phosphotransfer, compromised the contractility-coronary flow relationship, and precipitated inadequate coronary reflow following ischemia-reperfusion. Deficit in adenylate kinase activity abrogated AMP signal generation and reduced the vascular adenylate kinase/creatine kinase activity ratio essential for the response of metabolic sensors. The sarcolemma-associated splice variant AK1β facilitated adenosine production, a function lost in the absence of adenylate kinase activity. Adenosine treatment bypassed AK1 deficiency and restored post-ischemic flow to wild-type levels, achieving phenotype rescue. AK1 phosphotransfer thus transduces stress signals into adequate vascular response, providing linkage between cell bioenergetics and coronary flow.