Miracle-dz/UniFAR-FTUs huggingface dataset:
Isolation and characterization of engine oil degrading indigenous microrganisms in Kwazulu-Natal, South Africa

As the usage of petroleum hydrocarbon products increases, soil contamination with diesel and engine oils is becoming one of the major environmental problems. To investigate the countermeasure to remediate soils contaminated with oils, bioremediation provide an effective and efficient strategy to speed up the clean-up processes. Three bacterial isolates capable of utilizing used engine-oil as a carbon source were isolated from contaminated soils using the enrichment technique. Three isolates were identified as Flavobacterium sp. , Acinetobacterium calcoaceticum and Pseudomonas aeruginosa based on biochemical tests and 16S rRNA sequencing. The gavimetric analysis revealed that A. calcoaceticum and a consortium of the isolates were capable of utilizing 80 and 90% of used engine oil, respectively, under laboratory conditions at 30°C and 160 rpm with Bushnell-Haas media in a 4 week period. An increase in oil degradation is correlated to an increase in cell number indicating that the bacterial isolates were responsible for the oil degradation. All isolates were capable of degrading the nparaffin up to 80% in a 2 week period. The optimal temperatures at which biodegradation occurred at 30–37°C. The preference of nitrogen sources and minimal salts were different for different bacterial isolates. The results obtained demonstrate the potential for oil bioremediation of these isolates in situ and/or ex situ.
Evolution of the Dinosauriform Respiratory Apparatus: New Evidence from the Postcranial Axial Skeleton

Examination of the thoracic rib and vertebral anatomy of extant archosaurs indicates a relationship between the postcranial axial skeleton and pulmonary anatomy. Lung ventilation in extant crocodilians is primarily achieved with a hepatic piston pump and costal rotation. The tubercula and capitula of the ribs lie on the horizontal plane, forming a smooth thoracic “ceiling” facilitating movement of the viscera. Although the parietal pleura is anchored to the dorsal thoracic wall, the dorsal visceral pleura exhibits a greater freedom of movement. The air sac system and lungs of birds are associated with bicapitate ribs with a ventrally positioned capitular articulation, generating a rigid and furrowed rib cage that minimizes dorsoventral changes in volume in the dorsal thorax. The thin walled bronchi are kept from collapsing by fusion of the lung to the thorax on all sides. Data from this study suggest a progression from a dorsally rigid, heterogeneously partitioned, multichambered lung in basal dinosauriform archosaurs towards the small entirely rigid avian‐style lung that was likely present in saurischian dinosaurs, consistent with a constant volume cavum pulmonale, thin walled parabronchi, and distinct air sacs. There is no vertebral evidence for a crocodilian hepatic piston pump in any of the taxa reviewed. The evidence for both a rigid lung and unidirectional airflow in dinosauriformes raises the possibility that these animals had a highly efficient lung relative to other Mesozoic vertebrates, which may have contributed to their successful radiation during this time period. Anat Rec, 2011. © 2011 Wiley‐Liss, Inc.
Food spoilage, food infections and intoxications caused by microorganisms and methods for their detection

CONTENTS Introduction Food Spoilage and General Principles Underlying Spoilage of Food Intrinsic Parameters Extrinsic Parameters Microbial Spoilage of Foods Spoilage of fresh and ready-to-eat meat products Spoilage of milk and milk products Spoilage of fruits and vegetables Spoilage of canned foods Major Food Borne Infections/ Intoxications Caused by Bacteria General Control Measures for Prevention of Food Borne Diseases Microbial Testing of Foods Conventional Methods Rapid Detection of Emerging High Risk Pathogens in Foods
Learning Analytics: A Case Study of the Process of Design of Visualizations

The ability to visualize student engagement and experience data provides valuable opportunities for learning support and curriculum design. With the rise of the use of learning analytics to provide “actionable intelligence” [1] on students’ learning, the challenge is to create visualisations of the data which are clear and useful to the intended audience. This process of finding the best way to visually represent data is often iterative, with many different designs being trialled before the final design is settled upon. This paper presents a case study of the process of refining a visualization of students’ learning experience data. In this case the aim was to create a visual representation of the continuity of care students were exposed to during a longitudinal placement as part of a medical degree. The process of visualization refinement is outlined as well as the lessons learnt along the way.
Oxidant stress, mitochondria, and cell death mechanisms in drug-induced liver injury: Lessons learned from acetaminophen hepatotoxicity

Hepatotoxicity is a serious problem during drug development and for the use of many established drugs. For example, acetaminophen overdose is currently the most frequent cause of acute liver failure in the United States and Great Britain. Evaluation of the mechanisms of drug-induced liver injury indicates that mitochondria are critical targets for drug toxicity, either directly or indirectly through the formation of reactive metabolites. The consequence of these modifications is generally a mitochondrial oxidant stress and peroxynitrite formation, which leads to structural alterations of proteins and mitochondrial DNA and, eventually, to the opening of mitochondrial membrane permeability transition (MPT) pores. MPT pore formation results in a collapse of mitochondrial membrane potential and cessation of adenosine triphosphate synthesis. In addition, the release of intermembrane proteins, such as apoptosis-inducing factor and endonuclease G, and their translocation to the nucleus, leads to nuclear DNA fragmentation. Together, these events trigger necrotic cell death. Alternatively, the release of cytochrome c and other proapoptotic factors from mitochondria can promote caspase activation and apoptotic cell death. Drug toxicity can also induce an inflammatory response with the formation of reactive oxygen species by Kupffer cells and neutrophils. If not properly detoxified, these extracellularly generated oxidants can diffuse into hepatocytes and trigger mitochondrial dysfunction and oxidant stress, which then induces MPT and necrotic cell death. This review addresses the formation of oxidants and the defense mechanisms available for cells and applies this knowledge to better understand mechanisms of drug hepatotoxicity, especially acetaminophen-induced liver injury.
Poster: fast, automatic iPhone shoulder surfing

Touchscreen devices increase the risk of shoulder surfing to such an extent that attackers could steal sensitive information by simply following the victim and observe his or her portable device. We underline this concern by proposing an automatic shoulder surfing attack against modern touchscreen keyboards that display magnified keys in predictable positions. We demonstrate this attack against the Apple iPhone - although it can work with other layouts and different devices - and show that it recognizes up to 97.07% (91.03% on average) of the keystrokes, with only 1.15% of errors, at 37 to 51 keystrokes per minute: About eight times faster than a human analyzing a recorded video. Our attack, described thoroughly in [2], accurately recovers the sequence of keystrokes input by the user. The attack described in [1], which targeted desktop scenarios and thus worked with very restrictive settings, is similar in spirit to ours. However, as it assumes that camera and target keyboard are both in fixed, perpendicular position, it cannot suite mobile settings, characterized by moving target and skewed, rotated viewpoints. Our attack, instead, requires no particular settings and even allows for natural movements of both target device and shoulder surfer's camera. In addition, our attack yields accurate output without any grammar or syntax checks, so that it can detect large context-free text or non-dictionary words. In summary: - We are the first studying the practical risks brought forth by mainstream touchscreen keyboards. - We design a practical attack that detects keystrokes on modern touchscreen keyboards: The attacker requires not to stand exactly behind the victim nor to observe the screen perpendicularly. Our attack is robust to occlusions (eg, typing fingers), thanks to our efficient filtering technique that validates detected keys and reconstructs keystroke sequences accurately.
Syntactic patterns in classical Chinese poems: A quantitative study

It is widely believed that different parts of a classical Chinese poem vary in syntactic properties. The middle part is usually parallel, i.e. the two lines in a couplet have similar sentence structure and part of speech; in contrast, the beginning and final parts tend to be non-parallel. Imagistic language, dominated by noun phrases evoking images, is concentrated in the middle; propositional language, with more complex grammatical structures, is more often found at the end. We present the first quantitative analysis on these linguistic phenomena—syntactic parallelism, imagistic language, and propositional language—on a treebank of selected poems from the Complete Tang Poems . Written during the Tang Dynasty between the 7th and 9th centuries CE, these poems are often considered the pinnacle of classical Chinese poetry. Our analysis affirms the traditional observation that the final couplet is rarely parallel; the middle couplets are more frequently parallel, especially at the phrase rather than the word level. Further, the final couplet more often takes a non-declarative mood, uses function words, and adopts propositional language. In contrast, the beginning and middle couplets employ more content words and tend toward imagistic language.
Interhemispheric Cortical Inhibition Is Reduced in Young Adults With Developmental Coordination Disorder

Introduction While the etiology of developmental coordination disorder (DCD) is yet to be established, brain-behavior modeling provides a cogent argument that neuropathology may subserve the motor difficulties typical of DCD. We argue that a number of the core behavioral features of the DCD profile (such as poor surround inhibition, compromised motor inhibition, and the presence of mirror movements) are consistent with difficulties regulating inhibition within the primary motor cortex (M1). This study aimed to be the first account of the integrity of cortical inhibition in motor cortices in DCD. Method The sample consisted of eight adults with DCD aged (18–30 years) and 10 aged matched neurotypical controls. Participants received a common battery of single and paired-pulse transcranial magnetic stimulation from which a series of neurophysiological measures classically used to measure intra- [e.g., short-interval cortical inhibition (SICI), long-interval cortical inhibition (LICI), and cortical silent period] and inter hemispheric [e.g., ipsilateral silent period (ISP)] cortical inhibition of the M1 at rest were recorded. Results While no group differences were observed for any measure of intrahemispheric cortical inhibition, individuals with DCD demonstrated significantly reduced interhemispheric cortical inhibition relative to controls, shown by consistently lower ISPratios. Conclusion Our findings are consistent with the view that regulation of cortical inhibition of M1 activity may be atypical in individuals with DCD, indicating differential GABAergic operation. This effect, however, appears to be select to cortical inhibition. Importantly, our data support the notion that reduced interhemispheric M1 cortical inhibition may at least partly explain commonly reported difficulties with bimanual motor control in DCD. The neurochemical implications and limitations of this evidence will be discussed.
Assisted Coverage

The malfunction of safety-critical systems may cause damage to people and the environment. Software within those systems is rigorously designed and verified according to domain specific guidance, such as ISO26262 for automotive safety. This paper describes academic and industrial co-operation in tool development to support one of the most stringent of the requirements — achieving full code coverage in requirements-driven testing. We present a verification workflow supported by a tool that integrates the coverage measurement tool RapiCover with the test-vector generator FShell. The tool assists closing the coverage gap by providing the engineer with test vectors that help in debugging coverage-related code quality issues and creating new test cases, as well as justifying the presence of unreachable parts of the code in order to finally achieve full effective coverage according to the required criteria. To illustrate the practical utility of the tool, we report about an application of the tool to a case study from automotive industry.
On combining gait features

This paper describes a method of gait recognition using multiple gait features in conjunction with score-level fusion techniques. More specifically, we focus on the state-of-the-art period-based gait features such as a gait energy image, a frequency-domain feature, a gait entropy image, a chrono-gait image, and a gait flow image. In addition, we employ various types of the score-level fusion approaches including not only conventional transformation-based approaches (e.g., sum-rule and min-rule) but also classification-based approaches (e.g., support vector machine) and density-based approaches (e.g., Gaussian mixture model, kernel density estimation, linear logistic regression). In experiments, the large-population gait database with 3,249 subjects was used to measure the performance improvement in a statistically reliable way. The experimental results show 7% relative improvement on average with regard to equal error rate of the false acceptance rate and false rejection rate in verification scenarios, and also show 20% reduction of the number of candidates to be checked under 1% misdetection rate on average in screening tasks.
Toward a Differential Diagnosis of Hidden Hearing Loss in Humans

Recent work suggests that hair cells are not the most vulnerable elements in the inner ear; rather, it is the synapses between hair cells and cochlear nerve terminals that degenerate first in the aging or noise-exposed ear. This primary neural degeneration does not affect hearing thresholds, but likely contributes to problems understanding speech in difficult listening environments, and may be important in the generation of tinnitus and/or hyperacusis. To look for signs of cochlear synaptopathy in humans, we recruited college students and divided them into low-risk and high-risk groups based on self-report of noise exposure and use of hearing protection. Cochlear function was assessed by otoacoustic emissions and click-evoked electrocochleography; hearing was assessed by behavioral audiometry and word recognition with or without noise or time compression and reverberation. Both groups had normal thresholds at standard audiometric frequencies, however, the high-risk group showed significant threshold elevation at high frequencies (10–16 kHz), consistent with early stages of noise damage. Electrocochleography showed a significant difference in the ratio between the waveform peaks generated by hair cells (Summating Potential; SP) vs. cochlear neurons (Action Potential; AP), i.e. the SP/AP ratio, consistent with selective neural loss. The high-risk group also showed significantly poorer performance on word recognition in noise or with time compression and reverberation, and reported heightened reactions to sound consistent with hyperacusis. These results suggest that the SP/AP ratio may be useful in the diagnosis of “hidden hearing loss” and that, as suggested by animal models, the noise-induced loss of cochlear nerve synapses leads to deficits in hearing abilities in difficult listening situations, despite the presence of normal thresholds at standard audiometric frequencies.
Effects of Dantrolene on Steps of Excitation-Contraction Coupling in Mammalian Skeletal Muscle Fibers

The effects of the muscle relaxant dantrolene on steps of excitation-contraction coupling were studied on fast twitch muscles of rodents. To identify the site of action of the drug, single fibers for voltage-clamp measurements, heavy SR vesicles for calcium efflux studies and solubilized SR calcium release channels/RYRs for lipid bilayer studies were isolated. Using the double Vaseline-gap or the silicone-clamp technique, dantrolene was found to suppress the depolarization-induced elevation in intracellular calcium concentration ([Ca2+]i) by inhibiting the release of calcium from the SR. The suppression of [Ca2+]i was dose-dependent, with no effect at or below 1 μM and a 53 ± 8% (mean ± SEM, n = 9, cut fibers) attenuation at 0 mV with 25 μM of extracellularly applied dantrolene. The drug was not found to be more effective if injected than if applied extracellularly. Calculating the SR calcium release revealed an equal suppression of the steady (53 ± 8%) and of the early peak component (46 ± 6%). The drug did not interfere with the activation of the voltage sensor in as much as the voltage dependence of both intramembrane charge movements and the L-type calcium currents (ICa) were left, essentially, unaltered. However, the inactivation of ICa was slowed fourfold, and the conductance was reduced from 200 ± 16 to 143 ± 8 SF−1 (n = 10). Dantrolene was found to inhibit thymol-stimulated calcium efflux from heavy SR vesicles by 44 ± 10% (n = 3) at 12 μM. On the other hand, dantrolene failed to affect the isolated RYR incorporated into lipid bilayers. The channel displayed a constant open probability for as long as 30–50 min after the application of the drug. These data locate the binding site for dantrolene to be on the SR membrane, but be distinct from the purified RYR itself.
The ARAMIS Workbench for Monitoring, Analysis and Visualization of Architectures based on Run-time Interactions

Up-to-date software architecture models dramatically ease the understanding and meaningful evolution of a software system. Unfortunately they are rarely available. Mostly the static view of the architecture is modeled and only stipulations are made regarding how architecture units should communicate. However, a software system tends to evolve independently from its description. This results in violations of the previously stipulated communication rules. A plethora of tools to recover up-to-date architecture models have been proposed, but little emphasis has been put on analyzing and validating the run-time interactions on various abstraction levels defined in the static view of the architecture. In our previous work we have presented ARAMIS - a conceptual infrastructure for the analysis and monitoring of data extracted during run-time - and some first evaluations thereof. This paper presents the current state of the ARAMIS Workbench, which automatically validates if the communication between the units of a software system matches its architecture model, provides visualizations of these interactions on higher and more understandable abstraction levels, and presents evaluations of the various units involved in the analyzed communication. We exemplify its capabilities on a case study based on the Carcass system used in teaching activities at our research group.
Mapping the Cargo Protein Membrane Translocation Step into the PEX5 Cycling Pathway*♦

Newly synthesized peroxisomal matrix proteins are targeted to the organelle by PEX5, the peroxisomal cycling receptor. Over the last few years, valuable data on the mechanism of this process have been obtained using a PEX5-centered in vitro system. The data gathered until now suggest that cytosolic PEX5·cargo protein complexes dock at the peroxisomal docking/translocation machinery, where PEX5 becomes subsequently inserted in an ATP-independent manner. This PEX5 species is then monoubiquitinated at a conserved cysteine residue, a mandatory modification for the next step of the pathway, the ATP-dependent dislocation of the ubiquitin-PEX5 conjugate back into the cytosol. Finally, the ubiquitin moiety is removed, yielding free PEX5. Despite its usefulness, there are many unsolved mechanistic aspects that cannot be addressed with this in vitro system and that call for a cargo protein-centered perspective instead. Here we describe a robust peroxisomal in vitro import system that provides this perspective. The data obtained with it suggest that translocation of a cargo protein across the peroxisomal membrane, including its release into the organelle matrix, occurs prior to PEX5 ubiquitination.
Analysis of Organic Aerosols Using a Micro-Orifice Volatilization Impactor Coupled to an Atmospheric-Pressure Chemical Ionization Mass Spectrometer

We present the development and characterization of a combination of a micro-orifice volatilization impactor (MOVI) and an ion trap mass spectrometer (IT/MS) with an atmospheric-pressure chemical ionization (APCI) source. The MOVI is a multi-jet impactor with 100 nozzles, allowing the collection of aerosol particles by inertial impaction on a deposition plate. The pressure drop behind the nozzles is approximately 5%, resulting in a pressure of 96 kPa on the collection surface for ambient pressures of 101.3 kPa. The cut-point diameter (diameter of 50% collection efficiency) is at 0.13 μm for a sampling flow rate of 10 L min–1. After the collection step, aerosol particles are evaporated by heating the impaction surface and transferred into the APCI-IT/MS for detection of the analytes. APCI was used in the negative ion mode to detect predominantly mono- and dicarboxylic acids, which are major oxidation products of biogenic terpenes. The MOVI-APCI-IT/MS instrument was used for the analysis of laboratory-generated secondary organic aerosol (SOA), which was generated by ozonolysis of α-pinene in a 100 L continuous-flow reactor under dark and dry conditions. The combination of the MOVI with an APCI-IT/MS improved the detection limits for small dicarboxylic acids, such as pinic acid, compared to online measurements by APCI-IT/MS. The limits of detection and quantification for pinic acid were determined by external calibration to 4.4 ng and 13.2 ng, respectively. During a field campaign in the southern Rocky Mountains (USA) in summer 2011 (BEACHON-RoMBAS), the MOVI-APCI-IT/MS was applied for the analysis of ambient organic aerosols and the quantification of individual biogenic SOA marker compounds. Based on a measurement frequency of approximately 5 h, a diurnal cycle for pinic acid in the sampled aerosol particles was found with maximum concentrations at night (median: 10.1 ng m−3) and minimum concentrations during the day (median: 8.2 ng m−3), which is likely due to the partitioning behavior of pinic acid and the changing phase state of the organic aerosol particles with changing relative humidity.