Miracle-dz/UniFAR-FTUs huggingface dataset:
The structure and function of small nucleolar ribonucleoproteins

Eukaryotes and archaea use two sets of specialized ribonucleoproteins (RNPs) to carry out sequence-specific methylation and pseudouridylation of RNA, the two most abundant types of modifications of cellular RNAs. In eukaryotes, these protein–RNA complexes localize to the nucleolus and are called small nucleolar RNPs (snoRNPs), while in archaea they are known as small RNPs (sRNP). The C/D class of sno(s)RNPs carries out ribose-2′-O-methylation, while the H/ACA class is responsible for pseudouridylation of their RNA targets. Here, we review the recent advances in the structure, assembly and function of the conserved C/D and H/ACA sno(s)RNPs. Structures of each of the core archaeal sRNP proteins have been determined and their assembly pathways delineated. Furthermore, the recent structure of an H/ACA complex has revealed the organization of a complete sRNP. Combined with current biochemical data, these structures offer insight into the highly homologous eukaryotic snoRNPs.
Results of the reconstructed MEDEBIS

The electron beam ion source (EBIS) can deliver sufficiently short and intense pulses of fully stripped light ions for single turn injection into a dedicated synchrotron for hadron therapy. The technology of such a MEDEBIS resembles travelling wave tubes used in satellites and can also be designed for lifetimes up to ten years. In a first setup using a normal conducting solenoid of 0.75 T and a trap length of 0.25 m the source delivered high charge states of light ions like O/sup 8+/, O/sup 7+/, O/sup 6+/ and C/sup 6+/, C/sup 5+/[1]. The fast ion extraction in less than 2 /spl mu/s is realised trough a special electrostatic structure providing a pulsed extraction potential gradient along the axis of the whole ion trap. The first results were very promising, but the residual gas pressure in the ionisation region was too high to make use of a sufficiently long confinement time in order to reach full abundance of bare nuclei. For the reconstructed MEDEBIS the inner two windings of the solenoid were drilled out to allow for a vacuum tube of about twice the diameter with better conductance. Together with the implementation of NEG getter material the residual gas pressure should be lowered sufficiently to reach the required yield of the fully stripped ions. Iron disks of high permeability have been added at both ends of the solenoid to increase the homogeneity of the magnetic field as well as to reduce the field in the gun and collector regions for a higher focussed current density in the trap region. The new MEDEBIS is under test and new experimental results will be presented.
The Questionable Merits Of Carbon Capture Readiness

Carbon capture and storage is accepted by money to play a major role in reducing future carbon dioxide emissions. Recently, many studies of new coaland gas-fired power plants have been conducted focusing o performance as well as cost. Due to the fact that t he technology is not yet commercially available or economically not reasonable and the need of new coal-fired power pla nts today causes a high increase in capacity of con ventional coalfired power plants. Therefore, capture-ready power plants with capture-ready investments are seen to b e an attractive solution enabling a later retrofit. The economic value of those investments has to be e valuated cautiously and depends on the time and the probability of the actual CCS-retrofit. In order to estimate the time and the probability, alternative echnical options available for switching from conventional coal-fire d power plants to CCS power plants have to be taken into account. Caused by the competition of those alternative opti ons, the retrofit of a capture-ready power plant mi ght be further delayed or even canceled. In our study, we compare three alternative technica l options, which are: First, retrofitting a modern (η = 47%) coal-fired power plant (capture-ready or non-capture-ready). S econd, the replacement of older power plants with a n efficiency between 35 and 40 percent (including an early shutdown) and the construction of a new CCS power plant . Third, the early shut-down of a modern power plant ( η = 47%) and construction of a new CCS power plant.
The Rat Game and the Mouse Game

We define three new take-away games, the Rat game, the Mouse game and the Fat Rat game. Three winning strategies are given for the Rat game and outlined for the Mouse and Fat Rat games. The efficiencies of the strategies are determined. Whereas the winning strategies of nontrivial take-away games are based on irrational numbers, our games are based on rational numbers. Another motivation stems from a problem in combinatorial number theory. 1 Description of the Game The Rat game is played on 3 piles of tokens by 2 players who play alternately. Positions in the game are denoted throughout in the form (x, y, z), with 0 ≤ x ≤ y ≤ z, and moves in the form (x, y, z) → (u, v, w), where of course also 0 ≤ u ≤ v ≤ w (see below). The player first unable to move — because the position is (0, 0, 0) — loses; the opponent wins. There are 3 types of moves: (I) Take any positive number of tokens from up to 2 piles. (II) Take ` > 0 from the x pile, k > 0 from the y pile, and an arbitrary positive number from the z pile, subject to the constraint |k − `| < a, where a = { 1 if y − x 6≡ 0 (mod 7) 2 if y − x ≡ 0 (mod 7). (III) Take ` > 0 from the x pile, k > 0 from the z pile, and an arbitrary positive number from the y pile, subject to the constraint |k − `| < b, where b = 3 if w = u; otherwise, b = { 5 if w − u 6≡ 4 (mod 7) 6 if w − u ≡ 4 (mod 7).
Testing an Emerging Paradigm in Migration Ecology Shows Surprising Differences in Efficiency between Flight Modes

To maximize fitness, flying animals should maximize flight speed while minimizing energetic expenditure. Soaring speeds of large-bodied birds are determined by flight routes and tradeoffs between minimizing time and energetic costs. Large raptors migrating in eastern North America predominantly glide between thermals that provide lift or soar along slopes or ridgelines using orographic lift (slope soaring). It is usually assumed that slope soaring is faster than thermal gliding because forward progress is constant compared to interrupted progress when birds pause to regain altitude in thermals. We tested this slope-soaring hypothesis using high-frequency GPS-GSM telemetry devices to track golden eagles during northbound migration. In contrast to expectations, flight speed was slower when slope soaring and eagles also were diverted from their migratory path, incurring possible energetic costs and reducing speed of progress towards a migratory endpoint. When gliding between thermals, eagles stayed on track and fast gliding speeds compensated for lack of progress during thermal soaring. When thermals were not available, eagles minimized migration time, not energy, by choosing energetically expensive slope soaring instead of waiting for thermals to develop. Sites suited to slope soaring include ridges preferred for wind-energy generation, thus avian risk of collision with wind turbines is associated with evolutionary trade-offs required to maximize fitness of time-minimizing migratory raptors.
Predicated static single assignment

Increases in instruction level parallelism are needed to exploit the potential parallelism available in future wide issue architectures. Predicated execution is an architectural mechanism that increases instruction level parallelism by removing branches and allowing simultaneous execution of multiple paths of control, only committing instructions from the correct path. In order for the compiler to expose such parallelism, traditional compiler data-flow analysis needs to be extended to predicated code. In this paper we present predicated static single assignment (PSSA) to enable aggressive predicated optimization and instruction scheduling. PSSA removes false dependences by exploiting renaming and information about the multiple control paths. We demonstrate the usefulness of PSSA for predicated speculation and control height reduction. These two predicated code optimizations used during instruction scheduling reduce the dependence length of the critical paths through a predicated region. Our results show that using PSSA to enable speculation and control height reduction reduces execution time from 10% to 58%.
Static Detection of Logic Vulnerabilities in Java Web Applications

Logic vulnerabilities occur when mistakes arise in the control flow associated to critical functionalities. We propose a lightweight static analysis approach to detect logic vulnerabilities in Java Web applications. The core idea of our approach is to discover deviant behaviors among duplication samples. Program slicing technique is leveraged to extract duplicated invocations targeted similar functionalities. Subsequently, path exploration is conducted to split slices into several path sensitive slices. Then we make comparison between any two similar slices on their path condition, and report the slices with abnormal path condition as logic vulnerabilities. We implemented our approach in a prototype tool named LVD (Logic Vulnerability Detector), and evaluated it on seven real world applications scaled from thousands to million lines of code. The evaluation results show that our approach achieves bigger coverage with acceptable cost and better scalability than previous approaches.
The Relationship between Serum Zinc Level and Preeclampsia: A Meta-Analysis

The association between serum zinc level and preeclampsia (PE) remains controversial. A systematic literature search was performed in PubMed, Web of Science and Embase for relevant available articles. The articles were limited to those in English from January 1990 to April 2015. Observational studies evaluating the association between serum zinc level and PE were included. The I2 was used to assess heterogeneity and the random effect model (REM) was adopted as the pooling method. The pooled standard mean difference (SMD) with 95% confidence interval (CI) was used to estimate the association between serum zinc level and PE. Seventeen observational studies were included. Compared with healthy pregnancy controls, PE patients have lower serum zinc level in 14 studies about total PE (SMD (95% CI): −0.587 (−0.963, −0.212), Z = 3.06, p for Z = 0.002; I2 = 88.4%, p for I2 < 0.0001). In subgroup analysis, a lower serum zinc level in PE patients compared with healthy pregnancy controls was observed in studies conducted in Asia, studies with zinc level measured in serum, and studies involving fasting participants. The SMD did not differ significantly between studies with healthy pregnancy controls matched by individual age (yes or no), and by individual gestational age (yes or no), respectively. Results from this meta-analysis indicate that serum zinc level in PE patients is significantly lower than that in healthy pregnancy controls. A moderate amount of zinc supplementation during pregnancy is advocated to reduce the incidence of PE.
Methoden der lexikalischen Nachkorrektur OCR-erfasster Dokumente

Das maschinelle Lesen, d. h. die Umwandlung gedruckter Dokumente via Pixelreprasentation in eine Symbolfolgen, erfolgt mit heute verfugbaren, kommerziellen OCR-Engines fur viele Dokumentklassen fast schon fehlerfrei. Trotzdem gilt fur die meisten OCR-Anwendungen die Devise, je weniger Fehler, desto besser. Beispielsweise kann ein falsch erkannter Name innerhalb eines Geschaftsbriefes in einem automatisierten System zur Eingangsspostverteilung unnotige Kosten durch Fehlzuordnungen o.a. verursachen. Eine lexikalische Nachkorrektur hilft, verbleibende Fehler von OCR-Engines aufzuspuren, zu korrigieren oder auch mit einer interaktiven Korrektur zu beseitigen. Neben einer Realisierung als nachgelagerte, externe Komponente, kann eine lexikalische Nachkorrektur auch direkt in eine OCR-Engine integriert werden. Meinen Beitrag zur lexikalischen Nachkorrektur habe ich in zehn Thesen untergliedert: These T1: Fur eine Nachkorrektur von OCR-gelesenen Fachtexten konnen Lexika, die aus thematisch verwandten Web-Dokumenten stammen, gewinnbringend eingesetzt werden. These T2: Das Vokabular eines Fachtexts wird von grosen Standardlexika unzureichend abgedeckt. Durch Textextraktion aus thematisch verwandten Web-Dokumenten lassen sich Lexika mit einer hoheren Abdeckungsrate gewinnen. Zudem spiegeln die Frequenzinformationen aus diesen Web-Dokumenten die des Fachtexts besser wider als Frequenzinformationen aus Standardkorpora. These T3: Automatisierte Anfragen an Suchmaschinen bieten einen geeigneten Zugang zu den einschlagigen Web-Dokumenten eines Fachgebiets. These T4: Eine feingliedrige Fehlerklassifikation erlaubt die Lokalisierung der beiden Hauptfehlerquellen der webgestutzten Nachkorrektur: • falsche Freunde, d. h. Fehler, die unentdeckt bleiben, da sie lexikalisch sind • ungluckliche Korrekturen hin zu Orthographie- oder Flexions-Varianten These T5: Falsche Freunde werden durch eine Kombination mehrerer OCR-Engines deutlich vermindert. These T6: Mit einfachen Heuristiken wird ein unglucklicher Variantenaustausch der Nachkorrekturkomponente vermieden. These T7: Mit einer Vereinheitlichung zu Scores lassen sich diverse OCR-Nachkorrekturhilfen wie etwa Wort-Abstandsmase, Frequenz- und Kontextinformationen kombinieren und zur Kandidaten- sowie Grenzbestimmung einsetzen. These T8: OCR-Nachkorrektur ist ein multidimensionales Parameteroptimierungsproblem, wie z. B. Auswahl der Scores, deren Kombination und Gewichtung, Grenzbestimmung oder Lexikonauswahl. Eine graphische Oberflache eignet sich fur eine Untersuchung der Parameter und deren Adjustierung auf Trainingsdaten. These T9: Die Software zur Parameteroptimierung der Nachkorrektur der Resultate einer OCR-Engine kann fur die Kombination mehrerer OCR-Engines wiederverwendet werden, indem die Einzelresultate der Engines wieder zu Scores vereinheitlicht werden. These T10: Eine Wort-zu-Wort-Alignierung, wie sie fur die Groundtruth-Erstellung und die Kombination von OCR-Engines notwendig ist, kann durch eine Verallgemeinerung des Levenshtein-Abstands auf Wortebene effizient realisiert werden.
Quercetin reduces cisplatin nephrotoxicity in rats without compromising its anti-tumour activity.

BACKGROUND Nephrotoxicity is the major limitation for the clinical use of cisplatin as an anti-tumoural drug. Our aim was to investigate the protective effect of quercetin on cisplatin nephrotoxicity in a rat tumour model in vivo and to examine the mechanisms of renal protection. METHODS Breast adenocarcinoma (13762 Mat B-III) cells were inoculated subcutaneously in male Fischer rats and 7 days later, the rats were administered daily with quercetin [50 mg/kg/day, intraperitoneally (i.p.)] or vehicle. Four days after that, the rats were given a single dose of cisplatin (4 mg/kg, i.p.) or vehicle. Tumour growth and renal function were monitored throughout the experiment. Two or 6 days after cisplatin administration, the rats were killed and the kidneys and tumours were removed to examine renal function and toxicity markers in both tissues. RESULTS In the kidney, cisplatin treatment induced: (i) a decrease in renal blood flow and glomerular filtration rate, (ii) tubular necrosis/apoptosis, (iii) increased lipid peroxidation and decreased endogenous antioxidant systems, (iv) increased expression of inflammation markers and (v) increased activity of the apoptosis executioner caspase-3. Cisplatin effectively reduced tumour size and weight. CONCLUSIONS Co-treatment with quercetin partially prevented all the renal effects of cisplatin, whereas it did not impair its anti-tumour activity. In conclusion, in a model of tumour-bearing rats, quercetin prevents the nephrotoxic effect of cisplatin without affecting its anti-tumour activity.
Sox9 sustains chondrocyte survival and hypertrophy in part through Pik3ca-Akt pathways

During endochondral bone formation, Sox9 expression starts in mesenchymal progenitors, continues in the round and flat chondrocyte stages at high levels, and ceases just prior to the hypertrophic chondrocyte stage. Sox9 is important in mesenchymal progenitors for their differentiation into chondrocytes, but its functions post-differentiation have not been determined. To investigate Sox9 function in chondrocytes, we deleted mouse Sox9 at two different steps after chondrocyte differentiation. Sox9 inactivation in round chondrocytes resulted in a loss of Col2a1 expression and in apoptosis. Sox9 inactivation in flat chondrocytes caused immediate terminal maturation without hypertrophy and with excessive apoptosis. Inactivation of Sox9 in the last few cell layers resulted in the absence of Col10a1 expression, suggesting that continued expression of Sox9 just prior to hypertrophy is necessary for chondrocyte hypertrophy. SOX9 knockdown also caused apoptosis of human chondrosarcoma SW1353 cells. These phenotypes were associated with reduced Akt phosphorylation. Forced phosphorylation of Akt by Pten inactivation partially restored Col10a1 expression and cell survival in Sox9floxdel/floxdel mouse chondrocytes, suggesting that phosphorylated Akt mediates chondrocyte survival and hypertrophy induced by Sox9. When the molecular mechanism of Sox9-induced Akt phosphorylation was examined, we found that expression of the PI3K subunit Pik3ca (p110α) was decreased in Sox9floxdel/floxdel mouse chondrocytes. Sox9 binds to the promoter and enhances the transcriptional activities of Pik3ca. Thus, continued expression of Sox9 in differentiated chondrocytes is essential for subsequent hypertrophy and sustains chondrocyte-specific survival mechanisms by binding to the Pik3ca promoter, inducing Akt phosphorylation.
Geochemical Distinction between Carbonate and Silicate Metasomatism in Generating the Mantle Sources of Alkali Basalts

Crustal metasomatism by subduction is considered as an important mechanism for generating mantle heterogeneity through infiltration of different metasomatic agents into the mantle. As a consequence of the subduction of oceanic crust (including oceanic basaltic rocks and seafloor sediments), both carbonate and silicate metasomatism are expected to occur at the slab–mantle interface in an oceanic subduction channel. This is demonstrated by an integrated study of major and trace elements, stable Mg-isotopes and radiogenic Sr–Nd–Hf isotopes in Cenozoic and Mesozoic alkali basalts from the West Qinling orogen, China. Although the two series of continental basalts show ocean island basalt (OIB)-like trace element distribution patterns and relatively depleted Sr– Nd–Hf isotope compositions, they exhibit differences in other geochemical variables. The Cenozoic basalts have low SiO2, but high CaO and MgO concentrations, and high CaO/Al2O3 ratios but low d Mg values of –0 54 to –0 32ø. They have relatively high abundances of melt-mobile incompatible trace elements such as the light rare earth elements (LREE) and most large ion lithophile elements (LILE), but low abundances of K, Pb, Zr, Hf and Ti, with high (La/Yb)N values but low Ti/Eu and Hf/Sm ratios. In contrast, the Mesozoic basalts have relatively high SiO2, but low CaO and MgO concentrations, and low CaO/Al2O3 ratios, but high d 26 Mg values of –0 35 to –0 21ø. They have relatively low abundances of melt-mobile incompatible trace elements such as the LILE and LREE, but are relatively enriched in Zr, Hf and Ti, with low (La/Yb)N values but high Ti/Eu and Hf/Sm ratios. These observations indicate a significant difference in the composition of the mantle sources between the two periods of alkali basalt magmatism. Whereas the low d Mg values of the Cenozoic basalts indicate the involvement of sedimentary carbonate in their mantle source, the high d Mg values of the Mesozoic basalts point to a primary contribution from a silicate component. Metasomatic reaction of depleted mid-ocean ridge basalt (MORB)-source mantle peridotite with carbonate and silicate melts, respectively, at the slab–mantle interface in the Paleotethyan oceanic subduction channel are responsible for the generation of their mantle sources. Both carbonate and silicate melts have been incorporated into the depleted MORB-source mantle wedge producing ‘crustal metasomatism’ in an oceanic subduction channel. We suggest that the type of metasomatic agent in the mantle sources is the key to the composition of the resultant alkali basalts.
Primates of the Caribbean: using historical-era introduction of monkeys in the Lesser Antilles to understand patterns of island evolution

Across the world, islands were and still are inhabited by unique species, often restricted to their own island and found nowhere else. After their ancestors managed to reach an island from a mainland population and become isolated from this mainland and its ecological restrictions, they often evolved spectacular adaptations. The more extrinsic barriers to gene flow there are and the more distant the populations, the greater the probability of a profound genetic and morphological change. Whereas many other insular mammalian taxa such as proboscideans, rodents and cervids react in readily identifiable trends, primates respond in varied and unpredictable ways. In order to better understand the underlying evolutionary principles behind island speciation, this thesis focuses on the small cercopithecine monkeys taken from western Africa to the Caribbean during the transatlantic slave trade. These Chlorocebus monkeys inhabit Nevis, St Kitts and Barbados but have long been assumed to originate solely from the Senegambia region. This thesis investigates the very early phase associated with island separation, using mitochondrial analysis and 3D geometric morphometric techniques to thoroughly assess whether any changes are present in these populations. An additional assessment is made of the three western African species of Chlorocebus, which is still largely subject to taxonomic discord. The results here show that the existing taxonomic status of African Chlorocebus does not fully describe the whole situation and that changes should be made to resolve this. The molecular results from this thesis show that rather than originating from one Senegambian location, Caribbean Chlorocebus monkeys instead originate from three different African species, across the entire western African coast, meaning their current designation as ‘African green monkeys’ is inaccurate. Additionally, morphological adaptations within these three insular populations are also already apparent, both across the three island groups and between Caribbean and African Chlorocebus.
Frontiers in Integrative Neuroscience Integrative Neuroscience

Noteworthy, previous electrophysiological studies described that some neurons in the lower bank STS respond to stimulation of several modalities or exhibit response modulation when a visual stimulus driving the neuron is paired with a stimulus in another modality (Benevento et al. previous studies were mostly descriptive and quantifi ed multi-sensory infl uences in terms of changes in fi ring rates. It hence remains unclear whether multisensory infl uences enhance the specifi city or reliability of neuron's responses and permit better discrimination of sensory stimuli, as would be expected from neural counterparts of perceptual benefi ts of sensory integration (Ernst and Bulthoff, 2004; Kayser et al., 2010). To directly assess the benefi ts of multisensory infl uences for neural representations in the lower bank STS, we quantifi ed the impact of simultaneously presented sounds on responses elicited by the presentation of naturalistic visual scenes. We used methods of information theory and stimulus decoding to quantify whether the responses of STS neurons become more reliable and informative in multisensory contexts. Such analysis can incorporate evidence from the full time course of each neurons response and hence avoids the need to interpret the possibly subtle modulations in particular response parameters, such as a neurons average (or peak) fi ring rate, or its latency. Our results demonstrate that STS neurons are sensitive to the congruency of auditory and visual