gebhart/patrepeval huggingface dataset:
hPSC-derived lung and intestinal organoids as models of human fetal tissue (2016)

In vitro human pluripotent stem cell (hPSC) derived tissues are excellent models to study certain aspects of normal human development. Current research in the field of hPSC derived tissues reveals these models to be inherently fetal-like on both a morphological and gene expression level. In this review we briefly discuss current methods for differentiating lung and intestinal tissue from hPSCs into individual 3-dimensional units called organoids. We discuss how these methods mirror what is known about in vivo signaling pathways of the developing embryo. Additionally, we will review how the inherent immaturity of these models lends them to be particularly valuable in the study of immature human tissues in the clinical setting of premature birth. Human lung organoids (HLOs) and human intestinal organoids (HIOs) not only model normal development, but can also be utilized to study several important diseases of prematurity such as respiratory distress syndrome (RDS), bronchopulmonary dysplasia (BPD), and necrotizing enterocolitis (NEC).
Deinococcus geothermalis: The Pool of Extreme Radiation Resistance Genes Shrinks (2007)

Bacteria of the genus Deinococcus are extremely resistant to ionizing radiation (IR), ultraviolet light (UV) and desiccation. The mesophile Deinococcus radiodurans was the first member of this group whose genome was completely sequenced. Analysis of the genome sequence of D. radiodurans, however, failed to identify unique DNA repair systems. To further delineate the genes underlying the resistance phenotypes, we report the whole-genome sequence of a second Deinococcus species, the thermophile Deinococcus geothermalis, which at its optimal growth temperature is as resistant to IR, UV and desiccation as D. radiodurans, and a comparative analysis of the two Deinococcus genomes. Many D. radiodurans genes previously implicated in resistance, but for which no sensitive phenotype was observed upon disruption, are absent in D. geothermalis. In contrast, most D. radiodurans genes whose mutants displayed a radiation-sensitive phenotype in D. radiodurans are conserved in D. geothermalis. Supporting the existence of a Deinococcus radiation response regulon, a common palindromic DNA motif was identified in a conserved set of genes associated with resistance, and a dedicated transcriptional regulator was predicted. We present the case that these two species evolved essentially the same diverse set of gene families, and that the extreme stress-resistance phenotypes of the Deinococcus lineage emerged progressively by amassing cell-cleaning systems from different sources, but not by acquisition of novel DNA repair systems. Our reconstruction of the genomic evolution of the Deinococcus-Thermus phylum indicates that the corresponding set of enzymes proliferated mainly in the common ancestor of Deinococcus. Results of the comparative analysis weaken the arguments for a role of higher-order chromosome alignment structures in resistance; more clearly define and substantially revise downward the number of uncharacterized genes that might participate in DNA repair and contribute to resistance; and strengthen the case for a role in survival of systems involved in manganese and iron homeostasis.
Uncertainty Estimation in a Vision-Based Tracking System (2006)

Vision-based tracking is concerned with the recovery of position and orientation data of moving objects based on visual input provided by one or more cameras. This paper describes a framework to handle geometric parameter uncertainties within a monocular outside-in vision-based tracking application. We present a sensor model - the stochastic camera - that is capable to take parameter calibration uncertainties into consideration even under real-time requirements. The feasibility of the proposed method is shown in closed-loop tracking experiments
Assembly of the Intrinsic Factor X Activating Complex – Interactions between Factor IXa, Factor VIIIa and Phospholipid (1985)

The activation of blood coagulation factor X by factor IXa is strongly stimulated by the non-enzymatic cofactors phospholipid, Ca2+ and activated factor VIII. In this paper we present a method by which we were able to determine binding affinities of factor IXa for phospholipids (either in the absence or presence of factor VIIIa) from kinetic measurements of factor X activation. It is shown that rates of factor X activation in the presence of phospholipids can be saturated with an excess factor VIIIa at limiting amounts of factor IXa and vice versa. Our data indicate that the enzymatic unit in the intrinsic factor X activator is a 1:1 stoichiometrical complex of factor IXa and factor VIIIa bound to phospholipid. Titrations with factor IXa at fixed concentrations of phospholipid and factor X show that the apparent dissociation constant of factor IXa for phospholipid is lowered from 10(-6) M to 10(-8) M by the presence of factor VIIIa. We conclude, that in analogy with the role of factor Va in prothrombin activation, phospholipid-bound factor VIIIa functions as a high-affinity binding site ("receptor") for factor IXa in the intrinsic factor X activating complex. Therefore, factor VIIIa increases the observed Vmax of factor X activation by 1) enhancing the kcat of the reaction and 2) increasing the amount of phospholipid-bound factor IXa that participates in factor X activation.
Diabetic Cardiomyopathy: Evidence, Mechanisms, and Therapeutic Implications (2004)

The presence of a diabetic cardiomyopathy, independent of hypertension and coronary artery disease, is still controversial. This systematic review seeks to evaluate the evidence for the existence of this condition, to clarify the possible mechanisms responsible, and to consider possible therapeutic implications. The existence of a diabetic cardiomyopathy is supported by epidemiological findings showing the association of diabetes with heart failure; clinical studies confirming the association of diabetes with left ventricular dysfunction independent of hypertension, coronary artery disease, and other heart disease; and experimental evidence of myocardial structural and functional changes. The most important mechanisms of diabetic cardiomyopathy are metabolic disturbances (depletion of glucose transporter 4, increased free fatty acids, carnitine deficiency, changes in calcium homeostasis), myocardial fibrosis (association with increases in angiotensin II, IGF-I, and inflammatory cytokines), small vessel disease (microangiopathy, impaired coronary flow reserve, and endothelial dysfunction), cardiac autonomic neuropathy (denervation and alterations in myocardial catecholamine levels), and insulin resistance (hyperinsulinemia and reduced insulin sensitivity). This review presents evidence that diabetes is associated with a cardiomyopathy, independent of comorbid conditions, and that metabolic disturbances, myocardial fibrosis, small vessel disease, cardiac autonomic neuropathy, and insulin resistance may all contribute to the development of diabetic heart disease.
Bio‐Refinery as the Bio‐Inspired Process to Bulk Chemicals (2007)

This paper describes several examples of knowledge-intensive technologies for the production of chemicals from biomass, which take advantage of the biomass structure in a more efficient way than the production of fuels or electricity alone. The depletion in fossil feedstocks, increasing oil prices, and the ecological problems associated with CO(2) emissions are forcing the development of alternative resources for energy, transport fuels, and chemicals, such as the replacement of fossil resources with CO(2) neutral biomass. Allied with this is the conversion of crude oil products utilizes primary products (ethylene, etc.) and their conversion into either materials or (functional) chemicals with the aid of co-reagents such as ammonia, by various process steps to introduce functionalities such as -NH(2) into the simple structures of the primary products. Conversely, many products found in biomass often contain functionalities. Therefore, it is attractive to exploit this in order to by-pass the use, and preparation of, co-reagents as well as to eliminate various process steps by utilizing suitable biomass-based precursors for the production of chemicals.
Beagle puppy model of intraventricular hemorrhage (1984)

The newborn beagle puppy has been demonstrated to provide a good model for neonatal intraventricular hemorrhage (IVH). A study was designed to determine if indomethacin can prevent IVH, and if indomethacin would produce changes in local cerebral glucose utilization (LCGU). By computerized random design, newborn beagle puppies were pretreated with either indomethacin (a known inhibitor of prostaglandin synthetase) or saline, and then assigned either to receive a hemorrhagic hypotension/volume reexpansion insult or to receive no insult. Pretreatment with indomethacin produced a marked drop in the incidence of IVH as well as significant alterations in the blood pressure responses to the hemorrhagic hypotension/volume reexpansion insult. Carbon-14 autoradiography was used to determine LCGU: no alterations were demonstrated in cerebral metabolism in uninjured pups pretreated with indomethacin compared to saline-pretreated animals. In addition, although the hemorrhagic hypotension/volume reexpansion insult produced marked alterations in LCGU in both groups of traumatized pups, indomethacin prevented the changes in LCGU in the germinal matrix and white matter that were found in the saline-pretreated animals.
The Putative Role of the Antiageing Protein Klotho in Cardiovascular and Renal Disease (2011)

Ageing is a multifactorial process often characterized by a progressive decline in physiological function(s). Ageing can and is often associated with an increased incidence of cardiovascular and renal disease. Klotho is a novel antiageing gene that encodes a protein with multiple pleiotropic functions including an emerging role in cardiorenal disease. Mice deficient for this gene display a phenotype of premature human ageing characterized by diffuse vascular calcification, altered calcium/phosphate metabolism, and shortened lifespan. Klotho is mainly expressed in the renal tubules but it also exists as circulating soluble form detectable in the blood, with systemic effects. Reduction in soluble Klotho has been associated with renal disease, hyperphosphataemia, increased oxidative stress, endothelial dysfunction, and diffuse vascular calcification. Conversely, overexpression of Klotho promotes cardiovascular-renal protection. The majority of the research on Klotho has been conducted in vitro and in animal studies but there is emerging data from human studies which suggest that Klotho may be a modifiable factor involved in the pathogenesis of cardiovascular and renal disease in at-risk populations. Further data is required to confirm if this novel protein can emerge as therapeutic tool that may be used to prevent or slow progression of cardiorenal disease.
Xsens MVN: Full 6DOF Human Motion Tracking Using Miniature Inertial Sensors (2009)

The Xsens MVN motion capture suit is an easy-to- use, cost efficient system for full-body human motion capture. MVN is based on unique, state-of-the-art miniature inertial sensors, biomechanical models and sensor fusion algorithms. MVN does not need external cameras, emitters or markers. It can thus be used outdoors as well as indoors, there are no restrictions for lighting, it does not suffer from problems of occlusion or missing markers. In addition, unique for inertial motion capture technology: the sensor-suit captures any type of movement, including running, jumping, crawling and cartwheels.
Johan Lagervist, After the Internet, Before Democracy: Competing Norms in Chinese Media and Society (2012)

The political implications of the Internet for authoritarian countries have become an important research agenda. In the case of authoritarian China, scholars have long explored the role of the Internet in Chinese politics. Some are rather pessimistic about its impact. They emphasize the reactive strategies to the Internet that the Chinese Communist Party (CCP) has adopted for its political stability (e.g., see Morozov, 2011). Other scholars are quite optimistic. They argue that the Internet has posed an instrumental threat to the Chinese authoritarian regime, and such a threat “arise[s] from Internet use by the mass public, civil society, the economy, and the international community” (Zheng & Wu, 2005, p. 510). John Lagerkvist, author of After the Internet, Before Democracy: Competing Norms in Chinese Media and Society, belongs to the optimistic camp. He argues that the Internet will lead to “a democratization of society and politics in China,” which will occur as the result of competition between the nation’s youth and the CCP over the construction of social norms (p. 263). In other words, the influence of the elite partystate norm over public opinion will be ultimately undermined by the oppositional youth/subaltern norm.
Deploying a wireless sensor network on an active volcano (2006)

Augmenting heavy and power-hungry data collection equipment with lighten smaller wireless sensor network nodes leads to faster, larger deployments. Arrays comprising dozens of wireless sensor nodes are now possible, allowing scientific studies that aren't feasible with traditional instrumentation. Designing sensor networks to support volcanic studies requires addressing the high data rates and high data fidelity these studies demand. The authors' sensor-network application for volcanic data collection relies on triggered event detection and reliable data retrieval to meet bandwidth and data-quality demands.
Prognostic factors for response and overall survival in 282 patients with higher-risk myelodysplastic syndromes treated with azacitidine (2010)

Prognostic factors for response and survival in higher-risk myelodysplastic syndrome patients treated with azacitidine (AZA) remain largely unknown. Two hundred eighty-two consecutive high or intermediate-2 risk myelodysplastic syndrome patients received AZA in a compassionate, patient-named program. Diagnosis was RA/RARS/RCMD in 4%, RAEB-1 in 20%, RAEB-2 in 54%, and RAEB-t (AML with 21%-30% marrow blasts) in 22%. Cytogenetic risk was good in 31%, intermediate in 17%, and poor in 47%. Patients received AZA for a median of 6 cycles (1-52). Previous low-dose cytosine arabinoside treatment (P = .009), bone marrow blasts > 15% (P = .004), and abnormal karyotype (P = .03) independently predicted lower response rates. Complex karyotype predicted shorter responses (P = .0003). Performance status ≥ 2, intermediate- and poor-risk cytogenetics, presence of circulating blasts, and red blood cell transfusion dependency ≥ 4 units/8 weeks (all P < 10(-4)) independently predicted poorer overall survival (OS). A prognostic score based on those factors discriminated 3 risk groups with median OS not reached, 15.0 and 6.1 months, respectively (P < 10(-4)). This prognostic score was validated in an independent set of patients receiving AZA in the AZA-001 trial (P = .003). Achievement of hematological improvement in patients who did not obtain complete or partial remission was associated with improved OS (P < 10(-4)). In conclusion, routine tests can identify subgroups of patients with distinct prognosis with AZA treatment.
Synthesis and Characterization of Colloidal CuInS2Nanoparticles from a Molecular Single-Source Precursor (2004)

Thermal decomposition of the molecular single-source precursor (PPh3)2CuIn(SEt)4 in the presence of hexanethiol in dioctylphthalate forms colloidal CuInS2 at 200 °C. The colloidal solution displays size-dependent quantum confinement behavior in the absorption and photoluminescence spectra. The average size of the nanocrystals can be increased from 2 to 4 nm by raising the reaction temperature from 200 °C to 250 °C. The nanoparticles are capped with hexanethiol ligands; these ligands can be exchanged with trioctylphosphine oxide or pyridine. The nature of the surface-capping ligands has a significant effect on the photoluminescence emission intensity. Investigation of the effect of synthesis parameters and postsynthesis treatments on the optical properties of the nanocrystals leads to the conclusion that the room-temperature emission originates in donor−acceptor defects.
One‐Year Experience with Candida Antigen Immunotherapy for Warts and Molluscum (2008)

Molluscum contagiosum and warts are two very common viral-induced diseases of childhood. We report our 1-year experience with intralesional candida antigen therapy for both warts and molluscum contagiosum. A retrospective chart review was performed and a total of 217 patients were identified. Follow-up was obtained either through clinic visits or telephone interviews for 25/47 molluscum patients and 55/170 wart patients. Of the molluscum patients with follow-up, 14/25 (56%) had complete resolution, 7/25 (28%) had partial clearing, and 4/25 (16%) had no improvement. For the wart patients with follow-up, 48/55 (87%) had complete resolution, 3/55 (6%) had partial clearing, and 4/55 (7%) had no improvement. It is important to note that our clearance rate may be overestimated, as many patients were also treated concurrently with liquid nitrogen or other therapies. All wart and molluscum patients experienced some discomfort at the time of injection, but no serious side effects were reported. Our experience suggests intralesional candida antigen may represent a treatment option for warts and molluscum contagiosum that is safe and effective.
Factors predicting mortality in emergency abdominal surgery in the elderly (2012)

Mortality in elderly patients who underwent emergency surgery for acute abdominal disease can be predicted using the disease scoring system (POSSUM) and on the basis of delay in hospital admission.
Reappearance of an embryonic pattern of fibronectin splicing during wound healing in the adult rat. (1989)

The adhesive extracellular matrix glycoprotein fibronectin (FN) is thought to play an important role in the cell migration associated with wound healing. Immunolocalization studies show abundant FN in healing wounds; however, these studies cannot define the cellular site(s) of FN synthesis, nor do they distinguish the different and potentially functionally distinct forms of FN that can arise from alternative splicing of the primary gene transcript. To examine these questions of FN synthesis and splicing during wound healing, we have performed in situ hybridization with segment-specific probes on healing wounds in adult rat skin. We find that the FN gene is expressed at increased levels after wounding both in the cells at the base of the wound and in subjacent muscle and dermis lateral to the wound. Interestingly, however, the pattern of splicing of FN mRNA was different in these areas. In adjacent dermis and muscle, the splicing pattern remains identical with that seen in normal adult rat skin, with two of the three spliced segments (EIIIA and EIIIB) excluded from FN mRNA. In contrast, these two segments are included in the FN mRNA present in the cells at the base of the wound. As a result, the mRNA in this region is spliced in a pattern identical with that found during early embryogenesis. The finding that the pattern of FN splicing during wound healing resembles an embryonic pattern suggests that alternative splicing may be used during wound healing as a mechanism to generate forms of FN that may be functionally more appropriate for the cell migration and proliferation associated with tissue repair.
Plasminogen deficiency leads to impaired remodeling after a toxic injury to the liver (1999)

Cellular proliferation and tissue remodeling are central to the regenerative response after a toxic injury to the liver. To explore the role of plasminogen in hepatic tissue remodeling and regeneration, we used carbon tetrachloride to induce an acute liver injury in plasminogen-deficient (Plg(o)) mice and nontransgenic littermates (Plg(+)). On day 2 after CCl(4), livers of Plg(+) and Plg(o) mice had a similar diseased pale/lacy appearance, followed by restoration of normal appearance in Plg(+) livers by day 7. In contrast, Plg(o) livers remained diseased for as long as 2.5 months, with a diffuse pale/lacy appearance and persistent damage to centrilobular hepatocytes. The persistent centrilobular lesions were not a consequence of impaired proliferative response in Plg(o) mice. Notably, fibrin deposition was a prominent feature in diseased centrilobular areas in Plg(o) livers for at least 30 days after injury. Nonetheless, the genetically superimposed loss of the Aalpha fibrinogen chain (Plg(o)/Fib(o) mice) did not correct the abnormal phenotype. These data show that plasminogen deficiency impedes the clearance of necrotic tissue from a diseased hepatic microenvironment and the subsequent reconstitution of normal liver architecture in a fashion that is unrelated to circulating fibrinogen.
Specific phenotypic restoration of an attenuated virus by knockout of a host resistance gene (2000)

To produce disease, viruses must enter the host, multiply locally in host tissues, spread from the site of entry, and overcome or evade host immune responses. At each stage in this infectious process, specific microbial and host genes determine the ultimate virulence of the virus. Genetic approaches have identified many viral genes that play critical roles in virulence and are presumed to target specific components of the host innate and acquired immune response. However, formal proof that a virulence gene targets a specific protein in a host pathway in vivo has not been obtained. Based on cell culture studies, it has been proposed that the herpes simplex virus type 1 gene ICP34.5 (ICP, infected cell protein) enhances neurovirulence by negating antiviral functions of the IFN-inducible double-stranded RNA-dependent protein kinase R or PKR [Chou, J., Chen, J.J., Gross, M. & Roizman, B. (1995) Proc. Natl. Acad. Sci. USA 92, 10516-10520]. Herein, we show that a virus that has been attenuated by deletion of ICP34.5 exhibits wild-type replication and virulence in a host from which the PKR gene has been deleted. We show that restoration of virulence is specific to ICP34.5 and PKR by using additional host and viral mutants. The use of recombinant viruses to infect animals with null mutations in host defense genes provides a formal genetic test for identifying in vivo mechanisms and targets of microbial virulence genes.