Miracle-dz/UniFAR-FTUs huggingface dataset:
Polymer scaling laws of unfolded and intrinsically disordered proteins quantified with single-molecule spectroscopy

The dimensions of unfolded and intrinsically disordered proteins are highly dependent on their amino acid composition and solution conditions, especially salt and denaturant concentration. However, the quantitative implications of this behavior have remained unclear, largely because the effective theta-state, the central reference point for the underlying polymer collapse transition, has eluded experimental determination. Here, we used single-molecule fluorescence spectroscopy and two-focus correlation spectroscopy to determine the theta points for six different proteins. While the scaling exponents of all proteins converge to 0.62 ± 0.03 at high denaturant concentrations, as expected for a polymer in good solvent, the scaling regime in water strongly depends on sequence composition. The resulting average scaling exponent of 0.46 ± 0.05 for the four foldable protein sequences in our study suggests that the aqueous cellular milieu is close to effective theta conditions for unfolded proteins. In contrast, two intrinsically disordered proteins do not reach the Θ-point under any of our solvent conditions, which may reflect the optimization of their expanded state for the interactions with cellular partners. Sequence analyses based on our results imply that foldable sequences with more compact unfolded states are a more recent result of protein evolution.
Feature Emphasis and Contextual Cutaways for Multimodal Medical Visualization

Dense clinical data like 3D Computed Tomography (CT) scans can be visualized together with real-time imaging for a number of medical intervention applications. However, it is difficult to provide a fused visualization that allows sufficient spatial perception of the anatomy of interest, as derived from the rich pre-operative scan, while not occluding the real-time image displayed embedded within the volume. We propose an importance-driven approach that presents the embedded data such that it is clearly visible along with its spatial relation to the surrounding volumetric material. To support this, we present and integrate novel techniques for importance specification, feature emphasis, and contextual cutaway generation. We show results in a clinical context where a pre-operative CT scan is visualized alongside a tracked ultrasound image, such that the important vasculature is depicted between the viewpoint and the ultrasound image, while a more opaque representation of the anatomy is exposed in the surrounding area.
Molecular and Cellular Pathobiology A Novel Transgenic Mouse Model of the Human Multiple Myeloma Chromosomal Translocation t ( 14 ; 16 ) ( q 32 ; q 23 )

Multiple myeloma (MM) is a currently incurable neoplasm of terminally differentiated B cells. The translocation and/or overexpression of c-MAF have been observed in human MM. Although c-MAF might function as an oncogene in human MM, there has been no report thus far describing the direct induction of MM by c-MAF overexpression in vivo. In this study, we have generated transgenic (TG) mice that express c-Maf specifically in the B-cell compartment. Aged c-Maf TG mice developed B-cell lymphomas with some clinical features that resembled those of MM, namely, plasma cell expansion and hyperglobulinemia. Quantitative RTPCR analysis demonstrated that Ccnd2 and Itgb7, which are known target genes of c-Maf, were highly expressed in the lymphoma cells. This novel TG mouse model of the human MM t(14;16)(q32;q23) chromosomal translocation should serve to provide new insight into the role of c-MAF in tumorigenesis. Cancer Res; 71(2);
The research on the active power filter based on the cascaded H-bridge converter

The model and the normal control method of the cascaded H-bridge active power filter is described firstly in this paper. However, problems exist in the normal control. One of the main problems is the unbalance of DC capacitor voltages of the H-bridge units. In this paper, an improved method for DC capacitor voltages control of the cascaded H-bridge active power filter is presented. With slightly shifting the modulation waves, it makes the DC capacitor voltages balancing in the accepted tolerance without any additional units. The method is validated by simulation and experiment.
Evolutionary Changes Affecting Rapid Identification of 2008 Newcastle Disease Viruses Isolated from Double-Crested Cormorants

ABSTRACT A morbidity-mortality event involving virulent Newcastle disease virus (NDV) in wild double-crested cormorants (Phalacrocorax auritus) occurred in North America in the summer of 2008. All 22 viruses isolated from cormorants were positively identified by the USDA-validated real-time reverse transcription-PCR assay targeting the matrix gene. However, the USDA-validated reverse transcription-PCR assay targeting the fusion gene that is specific for virulent isolates identified only 1 of these 22 isolates. Additionally, several of these isolates have been sequenced, and this information was used to identify genomic changes that caused the failure of the test and to revisit the evolution of NDV in cormorants. The forward primer and fusion probe were redesigned from the 2008 cormorant isolate sequence, and the revised fusion gene test successfully identified all 22 isolates. Phylogenetic analyses using both the full fusion sequence and the partial 374-nucleotide sequence identified these isolates as genotype V, with their nearest ancestor being an earlier isolate collected from Nevada in 2005. Histopathological analysis of this ancestral strain revealed morphological changes in the brain consistent with that of the traditional mesogenic pathotypes in cormorants. Intracerebral pathogenicity assays indicated that each of these isolates is virulent with values of >0.7 but not more virulent than earlier isolates reported from Canada.
Bupivacaine-Sufentanil Versus Bupivacaine-Fentanyl in Spinal Anesthesia of Patients Undergoing Lower Extremity Surgery

Background: The addition of intrathecal opioids to local anesthetics seems to improve the quality of analgesia and prolong the duration of analgesia, when using a subarachnoid block in Iranian patients with their specific pain tolerance. Objectives: The aim of this study was to evaluate the effects of adding fentanyl or sufentanil, to intrathecal bupivacaine, in terms of the onset and duration of; sensory block, motor block, hemodynamic effects and postoperative pain relief. Patients and Methods: This randomized clinical trial included 90 patients who underwent orthopedic lower limb surgeries. Subjects were divided into experimental groups; intrathecal fentanyl 25 µg (F), and sufentanil 2.5 µg (S), along with a placebo 0.5 mL normal saline (C) group, which were added to bupivacaine 0.5%, 15 mg. Duration of complete and effective analgesia was recorded (by a visual analogue scale-VAS). The pain scores were assessed postoperatively. Intraoperative mean arterial pressure (MAP), heart rate and oxygen saturation (SPO2) were recorded. The incidence of side effects such as; nausea, vomiting, pruritus, shivering, bradycardia and hypotension were also recorded. Results: MAP and heart rate results showed no significant changes at the designated time points among the three groups (P > 0.05). However, SPO2 and VAS showed significant changes at the designated time points among the three groups (P < 0.05). The duration of complete and effective analgesia was also significantly longer in the sufentanil group (P < 0.05). Motor block did not exhibit any significant difference (P = 0.67). Only pruritus as a side effect was significantly higher in the sufentanil group (P < 0.05), while all other evaluated side effects were significantly lower in the sufentanil group (P < 0.05). Conclusions: The addition of 2.5-3 mcg sufentanil to 15 mg 0.05% bupivacaine maintained the patient’s hemodynamic stability similar to fentanyl. Intrathecal sufentanil added to bupivacaine,when compared with fentanyl, may lead to prolonged duration of analgesia, facilitate the spread of the sensory block, increase mean SPO2 levels, and reduce overall side effects.
Usefulness of intraoperative electrical subcortical mapping during surgery for low-grade gliomas located within eloquent brain regions: functional results in a consecutive series of 103 patients.

OBJECT Although a growing number of authors currently advocate surgery to treat low-grade gliomas, controversy still persists, especially because of the risk of inducing neurological sequelae when the tumor is located within eloquent brain areas. Many researchers performing preoperative neurofunctional imaging and intraoperative electrophysiological methods have recently reported on the usefulness of cortical functional mapping. Despite the frequent involvement of subcortical structures by these gliomas, very few investigators have specifically raised the subject of fiber tracking. The authors in this report describe the importance of mapping cortical and subcortical functional regions by using intraoperative real-time direct electrical stimulations during resection of low-grade gliomas. METHODS Between 1996 and 2001, 103 patients harboring a corticosubcortical low-grade glioma in an eloquent area, with no or only mild deficit, had undergone surgery during which intraoperative electrical mapping of functional cortical sites and subcortical pathways was performed throughout the procedure. Both eloquent cortical areas and corresponding white fibers were systematically detected and preserved, thus defining the resection boundaries. Despite an 80% rate of immediate postoperative neurological worsening, 94% of patients recovered their preoperative status within 3 months--10% even improved--and then returned to a normal socioprofessional life. Eighty percent of resections were classified as total or subtotal based on control magnetic resonance images. CONCLUSIONS The use of functional mapping of the white matter together with cortical mapping allowed the authors to optimize the benefit/risk ratio of surgery of low-grade glioma invading eloquent regions. Given that preoperative fiber tracking with the aid of neuroimaging is not yet validated, we used intraoperative real-time cortical and subcortical stimulations as a valuable adjunct to the other mapping methods.
High GC Content Causes De Novo Created Proteins to be Intrinsically Disordered

De novo creation of protein coding genes involves formation of short ORFs from noncoding regions; some of these ORFs might then become fixed in the population. De novo created proteins need to, at the bare minimum, not cause serious harm to the organism, meaning that they should for instance not cause aggregation. Therefore, although the creation of the short ORFs could be truly random, but the fixation should be of subject to some selective pressure. The selective forces acting on de novo created proteins have been elusive and contradictory results have been reported. In Drosophila they are more disordered, i.e. are enriched in polar residues, than ancient proteins, while the opposite trend is present in yeast. To the best of our knowledge no valid explanation for this difference has been proposed. To solve this riddle we studied structural properties and age of all proteins in 187 eukaryotic species. We find that, on average, there are small differences between proteins of different ages, with the exception that younger proteins are shorter. However, when we take the GC content into account we find that this can explain the opposite trends observed in yeast (low GC) and drosophila (high GC). GC content is correlated with codons coding for disorder-promoting amino acids, and inversely correlated with transmembrane, helix and sheet promoting residues. We find that for the youngest proteins, i.e. the ones that are most likely to be de novo created, there exists a strong correlation with GC and structural properties. In contrast, this strong relationship is not seen for ancient proteins. This leads us to propose that structural features are not a strong determining factor for fixation of de novo created genes. Instead these proteins resemble random proteins given a particular GC level. The dependency on GC content is then gradually weakened during evolution. Author Summary We show that the GC content of a genomic area is of great importance for the properties of a protein-coding de novo created gene. The GC content affects the frequency of the codons and this affects the probability for each amino acid to be included in a de novo created protein. The codons encoding for Ala, Pro and Glu contain 80% GC, while codons for Lys, Phe, Asn, Tyr and Ile contain 20% or less. Pro and Gly are disorder-promoting, while Phe, Tyr and Ile are order-promoting. Therefore random protein sequences at a high GC will be more disordered than the ones created at a low GC. The structural properties of the youngest (orphan) proteins match to a large degree the properties of random proteins when the GC content is taken into account. In contrast structural properties of ancient proteins only show a weak correlation with GC content. This suggests that even after fixation of de novo created proteins largely resemble random proteins given a certain GC content. Thereafter, during evolution the correlation between structural properties and GC weakens.
Comparison of the chemical alteration trajectory of Liriodendron tulipifera L. leaf litter among forests with different earthworm abundance

[1] To investigate the control of earthworm populations on leaf litter biopolymer decay dynamics, we analyzed the residues of Liriodendron tulipifera L. (tulip poplar) leaves after six months of decay, comparing open surface litter and litter bag experiments among forests with different native and invasive earthworm abundances. Six plots were established in successional tulip poplar forests where sites varied in earthworm density and biomass, roughly 4–10 fold, of nonnative lumbricid species. Analysis of residues by diffuse reflectance Fourier transform infrared spectroscopy and alkaline CuO extraction indicated that open decay in sites with abundant earthworms resulted in residues depleted in cuticular aliphatic and polysaccharide components and enriched in ether-linked lignin relative to open decay in low earthworm abundance plots. Decay within earthworm-excluding litter bags resulted in an increase in aliphatic components relative to initial amendment and similar chemical trajectory to low earthworm open decay experiments. All litter exhibited a decline in cinnamyl-based lignin and an increase in nitrogen content. The influence of earthworm density on the chemical trajectory of litter decay was primarily a manifestation of the physical separation and concentration of lignin-rich and cutin-poor petioles with additional changes promoted by either microorganisms and/or mesofauna resulting in nitrogen addition and polysaccharide loss. These results illustrate how projected increases in invasive earthworm activity in northern North American forests could alter the chemical composition of organic matter in litter residues and potentially organic matter reaching the soil which may result in shifts in the aromatic and aliphatic composition of soils in different systems.
Optimizing Cue Effectiveness: Recall of 500 and 600 Incidentally Learned Words

In three cued recall experiments, prerequisites to optimal memory performance of large amounts of verbal materials were examined. Practically perfect recall of 500 and 600 words was obtained when effective retrieval cues were provided at test. The method used to demonstrate this was to instruct the subjects to define their own retrieval cues by generating properties or features to each word presented. At an unexpected recall test, these self-generated properties were presented as cues, and the subjects were instructed to recall the previously presented items. Cue effectiveness was manipulated by varying amount of retrieval information, type of cues, and retention interval. Distinctiveness and compatibility of retrieval cues are proposed as two necessary prerequisites to perfect recall performance. The well-known studies of Shepard (1967), Standing (1973), and Standing, Conezio, and Haber (1970) have shown extremely high recognition-memory performances of large amounts of pictorial information. Shepard (1967) presented subjects with 600 pictures for a few seconds each and then asked them which member of the various test pairs had been among the 600 items. More than 95% of the pictures presented previously were correctly recognized. At the time of publication, this result was found surprising by memory researchers, who were attuned to the rather meager ability of humans to remember nonmeaningful material such as nonsense syllables and isolated digits (Loftus, 1982). Although these studies are spectacular, it should, however, be pointed out that good memory performance per se is not an exceptional phenomenon in the memory literature. Mnemonic devices have been known to western culture for thousands of years (Yates, 1966), and several experiments have demonstrated that the capacity of human memory can be increased by using specific mnemonic systems (see, e.g., Bellezza, 1981) or some
Mother-Infant Attachment, Culture And Research: A Pilot Study

ABSTRACT The Strange Situation was developed in the United States in the 1970's as a measure of mother infant attachment. Since then there has been increased interest in its cross Cultural applicability. This paper reports on a pilot mother-infant intervention study conducted in Hanover Park, Cape Town. Its focus is on the attachment component of this study and its cross cultural relevance, highlights common shortcomings in the research and makes a number of suggestions about how to provide the data that will ensure meaningful attachment data in the South African context.
A fuzzy model for learning and adaptivity

Fuzzy models have been designed to represent approximate or imprecise relationships in complex systems and have been successfully employed in control systems, expert systems, and decision analysis. A hierarchical architecture for fuzzy modeling and inference has been developed to learn an initial set of rules from training data and allow adaptation of the rule base via system performance feedback. A general adaptive algorithm is presented and its performance examined for three types of adaptive behavior: continued learning, gradual change, and drastic change. In each of the three types of behavior, the adaptive algorithm has been shown to be able to reconfigure the rule bases to either improve the original approximation or adapt to the new system.
High accretion rate during class 0 phase due to external trigger

Recent observations indicate that some class 0 sources have accretion rates orders of magnitude higher than those of class I. We investigated the conditions for the high accretion rates of some class 0 sources by numerical calculations, modelling an external trigger. For no external trigger, we find that the maximum value of the accretion rate is determined by the ratio α of the gravitational energy to the thermal one within a flat inner region of the cloud core. The accretion rate reaches ∼10−4 M⊙ yr−1 if the cloud core has α≳ 2. For an external trigger, we find that the maximum value of the accretion rate is proportional to the momentum given to the cloud core. The accretion rate reaches ≳10−4 M⊙ yr−1 with a momentum of ∼0.1 M⊙ km s−1 when the initial central density of the cloud core is ∼10−18 g cm−3. A comparison between recent observational results for pre-stellar cores and our model with no triggered collapse indicates that the flat inner regions of typical pre-stellar cores are not large enough to cause accretion rates of ∼10−4 M⊙ yr−1. Our results show that the triggered collapse of the cloud core is more preferable for the origin of the high accretion rates of class 0 sources than no triggered collapse.
Memory Yield Improvement through Multiple Test Sequences and Application-Aware Fault Models

In this paper, we propose a way to improve the yield of memory products by selecting the appropriate test strategy for memory Built- in Self-Test (BIST). We argue that by testing the memory through a sequence of test algorithms which differ in their fault coverage, it is possible to bin the memory into multiple yield bins and increase the yield and product revenue. Further, the test strategy must take into consideration the usage model of the memory. Thus, a number of video and audio buffers are used in sequential access mode, but are overtested using conventional memory test algorithms which model a large number of defects which do not impact the operation of the buffers. We propose a binning strategy where memory test algorithms are applied in different order of strictness such that bins have a specific defect / fault grade. Depending on the applications some of these bins need not be discarded but sold at a lower price as the functionality would never catch the fault due to its usage of memory. We introduce the notion of a test map for the on-chip memories in a SoC and provide results of yield simulation on two specific test strategies called "Most Strict First" and "Least Strict First". Our simulations indicate that significant improvements in yield are possible through the adoption of the proposed technique. We show that the BIST controller area and run-time overheads also reduce when information about the usage model of the memory, such as sequential access, is exploited.
Cytoplasmic dynein-dependent vesicular transport from early to late endosomes [published erratum appears in J Cell Biol 1994 Feb;124(3):397]

We have used an in vitro fusion assay to study the mechanisms of transport from early to late endosomes. Our data show that the late endosomes share with the early endosomes a high capacity to undergo homotypic fusion in vitro. However, direct fusion of early with late endosomes does not occur. We have purified vesicles which are intermediates during transport from early to late endosomes in vivo, and analyzed their protein composition in two-dimensional gels. In contrast to either early or late endosomes, these vesicles do not appear to contain unique proteins. Moreover, these vesicles undergo fusion with late endosomes in vitro, but not with each other or back with early endosomes. In vitro, fusion of these endosomal vesicles with late endosomes is stimulated by polymerized microtubules, consistent with the known role of microtubules during early to late endosome transport in vivo. In contrast, homotypic fusion of early or late endosomes is microtubule-independent. Finally, this stimulation by microtubules depends on microtubule-associated proteins and requires the presence of the minus-end directed motor cytoplasmic dynein, but not the plus-end directed motor kinesin, in agreement with the microtubule organization in vivo. Our data strongly suggest that early and late endosomes are separate, highly dynamic organelles, which are connected by a microtubule-dependent vesicular transport step.
ased Methodology for the Design of CMOS Analog Circuits and Its Application to the Synthesis of a Silicon-on-Insulator

A new design methodology based on a unified treat- ment of all the regions of operation of the MOS transistor is proposed. It is intended for the design of CMOS analog circuits and especially suited for low power circuits where the moderate inversion region often is used because it provides a good compromise between speed and power consumption. The synthesis procedure is based on the relation between the ratio of the transconductance over dc drain current gm/ID and the normalized current Io /( W/L). The gm /ID indeed is a universal characteristic of all the transistors belonging to a same process. It may be derived from experimental measurements and fitted with simple analytical models. The method was applied successfully to the design of a silicon-on-insulator (SOI) micropower operational transconductance amplifier (OTA).