Miracle-dz/UniFAR-FTUs huggingface dataset:
The Fish Fauna of Lake Victoria during a Centruy of Human Induced Perturbations

witte, f. , kishe-machumu, m. a. , mkumbo, o. c. , wanink, J. h. , goudswaard, P. c. , van riJssel, J.c. & van oiJen, m. J.P. The fish fauna of Lake Victoria during a century of human induced perturbations. In J. Snoeks & A. Getahun (eds), Proceedings of the Fourth International Conference on African Fish and Fisheries, Addis Ababa, Ethiopia, 22-26 September 2008. Tervuren: Royal Museum for Central Africa, ‘Zoological Documentation Online Series’, pp. 49-66. Lake Victoria, by area the largest tropical lake of the world, is well-known for its diverse native fish fauna, which comprised about 500 endemic haplochromine cichlid species, two tilapiine species and 46 other species belonging to 12 families. During the past decades, the fish species diversity in the lake has declined dramatically due to human induced perturbations in the ecosystem. Based on literature and our own research findings we provide an overview of these changes and their most likely causes. During the first half of the last century, the increasing fishing pressure had a great impact on the native tilapiine cichlids and other large fish species. The shift in fish landings showed a classic example of fishing down the food web. Because of the dwindling catches, the Nile perch and four exotic tilapiine cichlids were introduced into the lake in the 1950s. Dramatic changes in the fish fauna occurred in the 1980s, with the upsurge of the introduced Nile perch and Nile tilapia, the decline of wetland zones, and increased eutrophication of the lake. The native tilapiines were replaced by the Nile tilapia, and several of the catfish species showed a dramatic decline, as did the lungfish. Most severely hit were the haplochromine cichlids, which disappeared from large parts of the lake, probably resulting in the extinction of many species. The introduced Nile perch and Nile tilapia, and the native cyprinid Rastrineobola argentea became the dominant fish species. Though water quality deteriorated and fish diversity decreased, fish landings rose from about 100,000 t y-1 in the 1970s to approximately 1 million t y-1 in the period 2005-2007. Since 1999 the biomass of Nile perch declined, whereas that of R. argentea increased. In the same period some of the sublittoral haplochromine species have recovered. Some of the surviving fish species, show remarkable changes in ecological and morphological features relative to the pre-Nile perch period, which seem to be adaptive responses to the changed environment. Although it may be possible to reconcile fisheries sustainability with biodiversity conservation in the lake basin, measures to reduce environmental stress in the lake are an urgent issue.
Recognizing 3D Objects using Ray-Triangle Intersection Distances

A novel method for recognizing 3D objects in an occluded, cluttered and noisy 2.5D scene, is presented. A ray-triangle intersection algorithm is used to compute distances between a circular sector that does not belong to the object and a triangulated surface. Firstly, for each sector's point its distance from the object is calculated and stored in a distance map. Secondly, a 2D histogram that counts the distance map's points whose corresponding distance falls within its distance bins, is formed. Then, the percentages of the bin points that fall within each bin are calculated forming the final descriptor vector. The same procedure is followed for the 2.5D scene. The number of the extracted descriptor vectors is independent to the number of the object's or scene's vertices. Experiments proved that the proposed method is fast, robust to noise, occlusion and clutter.
Erythritol feeds the pentose phosphate pathway via three new isomerases leading to D-erythrose-4-phosphate in Brucella

Significance Erythritol is a preferential substrate for Brucella, a common zoonotic bacterial pathogen. This four-carbon polyol is found in the reproductive organs of several affected species, a feature that may account for the characteristic viscerotropism of Brucella that leads to sterility and abortion. Although described previously as feeding glycolysis via dihydroxyacetone-phosphate, we show here that erythritol is actually converted into D-erythrose-4-phosphate through a hitherto undescribed set of reactions that involves three isomerases and that allows hexose-monophosphate synthesis and growth by feeding the pentose phosphate shunt. Elucidation of this unique carbohydrate pathway, which also applies to the Rhizobiales plant endosymbionts, opens the way for further research on the metabolic adaptation of an important facultative intracellular pathogen to target organs. Erythritol is an important nutrient for several α-2 Proteobacteria, including N2-fixing plant endosymbionts and Brucella, a worldwide pathogen that finds this four-carbon polyol in genital tissues. Erythritol metabolism involves phosphorylation to l-erythritol-4-phosphate by the kinase EryA and oxidation of the latter to l-3-tetrulose 4-phosphate by the dehydrogenase EryB. It is accepted that further steps involve oxidation by the putative dehydrogenase EryC and subsequent decarboxylation to yield triose-phosphates. Accordingly, growth on erythritol as the sole C source should require aldolase and fructose-1,6-bisphosphatase to produce essential hexose-6-monophosphate. However, we observed that a mutant devoid of fructose-1,6-bisphosphatases grew normally on erythritol and that EryC, which was assumed to be a dehydrogenase, actually belongs to the xylose isomerase superfamily. Moreover, we found that TpiA2 and RpiB, distant homologs of triose phosphate isomerase and ribose 5-phosphate isomerase B, were necessary, as previously shown for Rhizobium. By using purified recombinant enzymes, we demonstrated that l-3-tetrulose-4-phosphate was converted to d-erythrose 4-phosphate through three previously unknown isomerization reactions catalyzed by EryC (tetrulose-4-phosphate racemase), TpiA2 (d-3-tetrulose-4-phosphate isomerase; renamed EryH), and RpiB (d-erythrose-4-phosphate isomerase; renamed EryI), a pathway fully consistent with the isotopomer distribution of the erythrose-4-phosphate-derived amino acids phenylalanine and tyrosine obtained from bacteria grown on 13C-labeled erythritol. d-Erythrose-4-phosphate is then converted by enzymes of the pentose phosphate pathway to glyceraldehyde 3-phosphate and fructose 6-phosphate, thus bypassing fructose-1,6-bisphosphatase. This is the first description to our knowledge of a route feeding carbohydrate metabolism exclusively via d-erythrose 4-phosphate, a pathway that may provide clues to the preferential metabolism of erythritol by Brucella and its role in pathogenicity.
Notch inhibits Ptf1 function and acinar cell differentiation in developing mouse and zebrafish pancreas

Notch signaling regulates cell fate decisions in a variety of adult and embryonic tissues, and represents a characteristic feature of exocrine pancreatic cancer. In developing mouse pancreas, targeted inactivation of Notch pathway components has defined a role for Notch in regulating early endocrine differentiation, but has been less informative with respect to a possible role for Notch in regulating subsequent exocrine differentiation events. Here, we show that activated Notch and Notch target genes actively repress completion of an acinar cell differentiation program in developing mouse and zebrafish pancreas. In developing mouse pancreas, the Notch target gene Hes1 is co-expressed with Ptf1-P48 in exocrine precursor cells, but not in differentiated amylase-positive acinar cells. Using lentiviral delivery systems to induce ectopic Notch pathway activation in explant cultures of E10.5 mouse dorsal pancreatic buds, we found that both Hes1 and Notch1-IC repress acinar cell differentiation, but not Ptf1-P48 expression, in a cell-autonomous manner. Ectopic Notch activation also delays acinar cell differentiation in developing zebrafish pancreas. Further evidence of a role for endogenous Notch in regulating exocrine pancreatic differentiation was provided by examination of zebrafish embryos with homozygous mindbomb mutations, in which Notch signaling is disrupted. mindbomb-deficient embryos display accelerated differentiation of exocrine pancreas relative to wild-type clutchmate controls. A similar phenotype was induced by expression of a dominant-negative Suppressor of Hairless [Su(H)] construct, confirming that Notch actively represses acinar cell differentiation during zebrafish pancreatic development. Using transient transfection assays involving a Ptf1-responsive reporter gene, we further demonstrate that Notch and Notch/Su(H) target genes directly inhibit Ptf1 activity, independent of changes in expression of Ptf1 component proteins. These results define a normal inhibitory role for Notch in the regulation of exocrine pancreatic differentiation.
Protocol Offload Evaluation Using Simics

This paper describes our work with Simics (Magnusson, 2002) in the evaluation of protocol offloading to keep low the communication overheads on the host CPU. Simics is a platform that can be used for a functional system simulation, including the application program, the operating system, the protocol stack and the device drivers. Nevertheless, network-oriented applications require a full-system simulation that includes not only the OS code, but also a model of the memory system and a detailed timing model of network DMA effects (Binkert, 2003). As Simics does not provide a detailed network I/O model, it could present some limitations that make it difficult an accurate network-oriented full-system simulation. Here we present the way we have overcome this problem
A Novel Host-Proteome Signature for Distinguishing between Acute Bacterial and Viral Infections

Bacterial and viral infections are often clinically indistinguishable, leading to inappropriate patient management and antibiotic misuse. Bacterial-induced host proteins such as procalcitonin, C-reactive protein (CRP), and Interleukin-6, are routinely used to support diagnosis of infection. However, their performance is negatively affected by inter-patient variability, including time from symptom onset, clinical syndrome, and pathogens. Our aim was to identify novel viral-induced host proteins that can complement bacterial-induced proteins to increase diagnostic accuracy. Initially, we conducted a bioinformatic screen to identify putative circulating host immune response proteins. The resulting 600 candidates were then quantitatively screened for diagnostic potential using blood samples from 1002 prospectively recruited patients with suspected acute infectious disease and controls with no apparent infection. For each patient, three independent physicians assigned a diagnosis based on comprehensive clinical and laboratory investigation including PCR for 21 pathogens yielding 319 bacterial, 334 viral, 112 control and 98 indeterminate diagnoses; 139 patients were excluded based on predetermined criteria. The best performing host-protein was TNF-related apoptosis-inducing ligand (TRAIL) (area under the curve [AUC] of 0.89; 95% confidence interval [CI], 0.86 to 0.91), which was consistently up-regulated in viral infected patients. We further developed a multi-protein signature using logistic-regression on half of the patients and validated it on the remaining half. The signature with the highest precision included both viral- and bacterial-induced proteins: TRAIL, Interferon gamma-induced protein-10, and CRP (AUC of 0.94; 95% CI, 0.92 to 0.96). The signature was superior to any of the individual proteins (P<0.001), as well as routinely used clinical parameters and their combinations (P<0.001). It remained robust across different physiological systems, times from symptom onset, and pathogens (AUCs 0.87-1.0). The accurate differential diagnosis provided by this novel combination of viral- and bacterial-induced proteins has the potential to improve management of patients with acute infections and reduce antibiotic misuse.
Enterolactone Is Differently Associated with Estrogen Receptor β–Negative and –Positive Breast Cancer in a Swedish Nested Case-Control Study

Background: Differences in the estrogen receptor (ER) status of tumors may explain ambiguities in epidemiologic studies between the blood concentrations of enterolactone and breast cancer. To our knowledge, the association between enterolactone and ERβ-defined breast cancer has previously not been examined. Methods: A nested case-control study within the Malmö Diet and Cancer cohort used 366 cases and 733 matched controls to identify the major determinants of plasma enterolactone and to examine the association between enterolactone concentration and breast cancer risk and if this association differs depending on the ERα and ERβ status of tumors. A modified diet history method assessed dietary habits. Time-resolved fluoroimmunoassay determined enterolactone concentrations and immunohistochemistry using tissue microarray determined ER status. Results: Dietary fiber, as well as fruits and berries, and high-fiber bread showed statistically significant correlations with enterolactone (r, 0.13-0.22). Smoking and obesity were associated with lower enterolactone concentrations. Enterolactone concentrations above the median (16 nmol/L) were associated with reduced breast cancer risk when compared with those below [odds ratio, 0.75; 95% confidence interval (95% CI), 0.58-0.98]. The reduced risk was only observed for ERα [positive (+); odds ratio, 0.73; 95% CI, 0.55-0.97] and ERβ [negative (−)] tumors (odds ratio, 0.60; 95% CI, 0.42-0.84), with significantly different risks for ERβ (−) and ERβ (+) tumors (P for heterogeneity = 0.04). Conclusions: This study supports the suggestion that enterolactone is a biomarker of a healthy lifestyle. The protective association between enterolactone and breast cancer was significantly different between ERβ (−) and ERβ (+) tumors and most evident in tumors that express ERα but not ERβ. (Cancer Epidemiol Biomarkers Prev 2008;17(11):3241–51)
Elevated Frequency of Cataracts in Birds from Chernobyl

Background Radiation cataracts develop as a consequence of the effects of ionizing radiation on the development of the lens of the eye with an opaque lens reducing or eliminating the ability to see. Therefore, we would expect cataracts to be associated with reduced fitness in free-living animals. Methodology/Principal Findings We investigated the incidence of lens opacities typical of cataracts in more than 1100 free-living birds in the Chernobyl region in relation to background radiation. The incidence of cataracts increased with level of background radiation both in analyses based on a dichotomous score and in analyses of continuous scores of intensity of cataracts. The odds ratio per unit change in the regressor was 0.722 (95% CI 0.648, 0.804), which was less than odds ratios from investigations of radiation cataracts in humans. The relatively small odds ratio may be due to increased mortality in birds with cataracts. We found a stronger negative relationship between bird abundance and background radiation when the frequency of cataracts was higher, but also a direct effect of radiation on abundance, suggesting that radiation indirectly affects abundance negatively through an increase in the frequency of cataracts in bird populations, but also through direct effects of radiation on other diseases, food abundance and interactions with other species. There was no increase in incidence of cataracts with increasing age, suggesting that yearlings and older individuals were similarly affected as is typical of radiation cataract. Conclusions/Significance These findings suggest that cataracts are an under-estimated cause of morbidity in free-living birds and, by inference, other vertebrates in areas contaminated with radioactive materials.
Maximum Mean Discrepancy Imitation Learning

Imitation learning is an efficient method for many robots to acquire complex skills. Some recent approaches to imitation learning provide strong theoretical performance guarantees. However, there remain crucial practical issues, especially during the training phase, where the training strategy may require execution of control policies that are possibly harmful to the robot or its environment. Moreover, these algorithms often require more demonstrations than necessary to achieve good performance in practice. This paper introduces a new approach called Maximum Mean Discrepancy Imitation Learning that uses fewer demonstrations and safer exploration policy than existing methods, while preserving strong theoretical guarantees on performance. We demonstrate empirical performance of this method for effective navigation control of a social robot in a populated environment, where safety and efficiency during learning are primary considerations.
Hardware-Oblivious Parallelism for In-Memory Column-Stores

The multi-core architectures of today's computer systems make parallelism a necessity for performance critical applications. Writing such applications in a generic, hardware-oblivious manner is a challenging problem: Current database systems thus rely on labor-intensive and error-prone manual tuning to exploit the full potential of modern parallel hardware architectures like multi-core CPUs and graphics cards. We propose an alternative design for a parallel database engine, based on a single set of hardware-oblivious operators, which are compiled down to the actual hardware at runtime. This design reduces the development overhead for parallel database engines, while achieving competitive performance to hand-tuned systems. We provide a proof-of-concept for this design by integrating operators written using the parallel programming framework OpenCL into the open-source database MonetDB. Following this approach, we achieve efficient, yet highly portable parallel code without the need for optimization by hand. We evaluated our implementation against MonetDB using TPC-H derived queries and observed a performance that rivals that of MonetDB's query execution on the CPU and surpasses it on the GPU. In addition, we show that the same set of operators runs nearly unchanged on a GPU, demonstrating the feasibility of our approach.
Identification of Novel β1 Integrin Binding Sites in the Type 1 and Type 2 Repeats of Thrombospondin-1*

In addition to the three known β1 integrin recognition sites in the N-module of thrombospondin-1 (TSP1), we found that β1 integrins mediate cell adhesion to the type 1 and type 2 repeats. The type 1 repeats of TSP1 differ from typical integrin ligands in that recognition is pan-β1-specific. Adhesion of cells that express one dominant β1 integrin on immobilized type 1 repeats is specifically inhibited by antagonists of that integrin, whereas adhesion of cells that express several β1 integrins is partially inhibited by each α-subunit-specific antagonist and completely inhibited by combining the antagonists. β1 integrins recognize both the second and third type 1 repeats, and each type 1 repeat shows pan-β1 specificity and divalent cation dependence for promoting cell adhesion. Adhesion to the type 2 repeats is less sensitive to α-subunit antagonists, but a β1 blocking antibody and two disintegrins inhibit adhesion to immobilized type 2 repeats. β1 integrin expression is necessary for cell adhesion to the type 1 or type 2 repeats, and β1 integrins bind in a divalent cation-dependent manner to a type 1 repeat affinity column. The widely used TSP1 function blocking antibody A4.1 binds to a site in the third type 2 repeat. A4.1 proximally inhibits β1 integrin-dependent adhesion to the type 2 repeats and indirectly inhibits integrin-dependent adhesion mediated by the TSP1 type 1 repeats. Although antibody A4.1 is also an antagonist of CD36 binding to TSP1, these data suggest that some biological activities of A4.1 result from antagonism of these novel β1 integrin binding sites.
Neoatherosclerosis after Drug-Eluting Stent Implantation: Roles and Mechanisms

In-stent neoatherosclerosis (NA), characterized by a relatively thin fibrous cap and large volume of yellow-lipid accumulation after drug-eluting stents (DES) implantation, has attracted much attention owing to its close relationship with late complications, such as revascularization and late stent thrombosis (ST). Accumulating evidence has demonstrated that more than one-third of patients with first-generation DES present with NA. Even in the advent of second-generation DES, NA still occurs. It is indicated that endothelial dysfunction induced by DES plays a critical role in neoatherosclerotic development. Upregulation of reactive oxygen species (ROS) induced by DES implantation significantly affects endothelial cells healing and functioning, therefore rendering NA formation. In light of the role of ROS in suppression of endothelial healing, combining antioxidant therapies with stenting technology may facilitate reestablishing a functioning endothelium to improve clinical outcome for patients with stenting.
Working Around BGP: An Improvement of BGP Session Maintenance

The border gateway protocol (BGP) is the routing protocol that glues together the global Internet. BGP makes use of a "managed session" to maintain a bidirectional error-free session over which reachability information is exchanged between autonomous systems (ASes) in the global Internet. Nevertheless, despite its great importance to BGP, this "managed session" suffers from some weaknesses such as a slow failure mechanism, which may represent a great deal of lost data, and some security problems. Besides, some important services to BGP are missed such as multi-session and broadcasting. To overcome these weaknesses, session maintenance should be separated from BGP protocol. Instead, a separate managed session protocol (MSP) should cope with session maintenance. Accordingly, we argue that our approach may reduce BGP design complexity, increase both BGP reliability and robustness, and lead to a routing system that is easier to manage. We also describe our prototype implementation and some evaluation details
Potential Angiotensin‐Converting Enzyme Inhibitor—Epoetin Alfa Interaction in Patients Receiving Chronic Hemodialysis

We compared epoetin alfa (EPO) dose requirements and hematocrit response in 17 patients receiving chronic hemodialysis at baseline and after 3 and 12 months of therapy with angiotensin‐converting enzyme (ACE) inhibitors (12 enalapril, 5 captopril). No acute processes were present (infection, hemorrhage, inflammation) at time of starting ACE inhibitor therapy. Mean (± SD) intravenous EPO dosages at zero, 3, and 12 months were 6012 ± 2575, 5800 ± 2026, and 5660 ± 2285 U 3 times/week (p=0.56), and mean differences were − 212 U for 0–3 months (95% CI −1310 to 886) and −713 U for 0–12 months (95% CI −2142 to 716). Mean ± SD hematocrits were 30.5 ± 3.9%, 31.6 ± 3.2%, and 34.2 ± 3.1% (p=0.01, zero vs 12 mo), and mean differences were 1.7% for 0–3 months (95% CI −1.41 to 4.81) and 3.85% for zero–12 months (95% CI 0.71–7). Our results indicate that ACE inhibitors do not increase EPO dose requirements or reduce hematocrits in these patients.
An Unstable Central Disk in the Superluminal Black Hole X-Ray Binary GRS 1915+105

We have analyzed the X-ray spectra of the microquasar GRS 1915+105, as observed with the Proportional Counter Array (PCA) on the Rossi X-Ray Timing Explorer, during periods of stable weak emission, outbursts, and rapid flaring. We find that the complicated X-ray intensity curve of this source can be described by the rapid removal and replenishment of matter forming the inner part of an optically thick accretion disk, probably caused by a thermal-viscous instability analogous to that operating in dwarf novae, but here driven by the Lightman-Eardley instability. We find that the mass accretion rate in quiescence is about 10-6 M☉ yr-1. Only a small fraction of the energy liberated by accretion is emitted as radiation. We suggest that most of this energy is advected into the black hole in the high-viscosity state of the outburst cycle.