Miracle-dz/UniFAR-FTUs huggingface dataset:
Orientational distributions of contact clusters in proteins closely resemble those of an icosahedron

The orientational geometry of residue packing in proteins was studied in the past by superimposing clusters of neighboring residues with several simple lattices (Bagci et al., Proteins 2003;53:56–67; Raghunathan et al., Protein Sci 1997;6:2072–2083). In this work, instead of a lattice we use the regular polyhedron, the icosahedron, as the model to describe the orientational distribution of contacts in clusters derived from a high‐resolution protein dataset (522 protein structures with high resolution < 1.5 Å). We find that the order parameter (orientation function) measuring the angular overlap of directions in coordination clusters with directions of the icosahedron is 0.91, which is a significant improvement in comparison with the value 0.82 for the order parameter with the face‐centered cubic (fcc) lattice. Close packing tendencies and patterns of residue packing in proteins are considered in detail and a theoretical description of these packing regularities is proposed. Proteins 2008. © 2008 Wiley‐Liss, Inc.
The structure analysis of user behaviors for web traffic

Understanding the structure and dynamics of the behavior networks for web traffic that connect users with servers across the Internet is a key to modeling the network and designing future application. The Web-visited bipartite networks, called the user behavioral networks, display a natural bipartite structure: two kinds of nodes coexist with links only between nodes of different kinds. We obtained the result that the out-degree distribution of clients (the host initiating the connection), the in-degree distribution of servers (the host receiving the connection) and the strength distribution (the exchange bytes between clients and servers) is power-law, whose exponential is between 1.7 and 3.4. The clustering coefficient of clients and servers was larger than larger than in randomized, degree preserving versions of the same graph. At last, based on the algorithm of finding the community structure in bipartite network, we divided the clients into different interest communities. The structure analysis of user behavior for web traffic is very helpful for the network management, resource allocation, traffic engineering and security.
Characterization of the Antibody Response against NeuGcGM3 Ganglioside Elicited in Non-Small Cell Lung Cancer Patients Immunized with an Anti-Idiotype Antibody1

1E10 mAb is an anti-Id murine mAb (Ab2 mAb) specific for an Ab1 mAb that reacts with NeuGc-containing gangliosides, sulfatides, and Ags expressed in some human tumors. In preclinical studies, this Ab2 Ab was able to mimic NeuGc-containing gangliosides only in animals lacking expression of these Ags in normal tissues. In this study, we report on the immune responses elicited in 20 non-small cell lung cancer patients treated with 1 mg of aluminum hydroxide-precipitated 1E10 mAb. In the hyperimmune sera from 16 of 20 patients, a strong specific Ab response of both IgM and IgG isotypes against NeuGcGM3 ganglioside was observed. Patient immune sera were able to induce complement-independent cell death of NeuGcGM3-expressing X63 murine myeloma target cells. Significant immunoreactivity to NeuGcGM3 was still detected after the complete abrogation of the reactivity against 1E10 mAb by the adsorption of patient sera with this Ab. We hypothesize that Id−Ag+ Abs could reflect the activation of an autologous idiotypic cascade into the patients. Both Id+Ag+ and Id−Ag+ fractions were separated by affinity chromatography and characterized. Although IgG isotype Abs were found in both fractions, IgM isotype Abs were found only in the Id−Ag+ fraction. Both Id+Ag+ and Id−Ag+ Abs were able to specifically recognize and induce cell death in NeuGcGM3-expressing X63 myeloma target cells. Patients that developed IgG and/or IgM Abs against NeuGcGM3 showed longer median survival times.
Review article: Emergency department assessment and management of stab wounds to the neck

A stab wound to neck is an infrequent but highly important presentation to the ED in Australasia. Injuries to the two large neurovascular bundles that are vital to life might occur with associated injuries to midline aerodigestive structures. A literature review was undertaken to discuss the assessment and management of this injury in the emergency medicine setting.
Optoelectronic Mixer with Low Up-conversion Loss and Wide Up-conversion Bandwidth by Use of Flip-Chip Bonding Near-Ballistic Uni-Traveling-Carrier Photodiode and Coupled-Line Filter

We demonstrated optoelectronic mixers, which are constructed from near-ballistic uni-traveling-carrier photodiodes and band-pass filters. By utilizing strong nonlinearity of electron ballistic-transport, such module achieves low-up-conversion-loss (4.3 dB) and wide-up-conversion-bandwidth (11 GHz) under high-optical-power injection (16.6 dBm) at 30 GHz.
Site chronology and a review of radiocarbon dates from Fiji

The earliest radiocarbon dates from the Central Pacific were obtained by Edward W. Gifford, on charcoal recovered from excavations at Vunda and Navatu on Viti Levu (Gifford 1951a, b), and the results were later used to outline the first culture sequence proposed for Fiji, by Roger Green (1963). Subsequent investigations by Frost (1970, 1979) and Best (1984) substantially increased the number of 14C results from the archipelago, and allowed a wider range of cultural attributes, such as settlement location, interaction pattern, subsistence economy and stone-tool types, to be age-correlated. This chapter is divided into two sections, with the first section reporting the radiocarbon and thermoluminescence dates obtained by the Early Prehistory of Fiji project (the EPF) between 1996 and 2000. There were 68 radiocarbon determinations from 13 prehistoric sites. Most dated deposits were from coastal or near-coast locations on Viti Levu (n=9), two sites were from Beqa Island, and two excavations were on Mago Island in the Lau Group. Six sites contained ceramics of Lapita style (some mixed with pottery of post-Lapita age), two sites had deposits of mid-sequence antiquity, and five sites had pottery and other items common in late-prehistoric sites dating to the last millennium. Results were used to construct a chronology for each site by assessing the reliability of each determination. In several deposits, the age of the oldest cultural remains was not able to be determined with radiocarbon because of extensive reworking of Lapita remains with more recent cultural materials.
Regulatory T and B Cells in Asthmatic Women: Variations From Pregnancy to Postpartum.

BACKGROUND AND OBJECTIVE Allergic asthma and rhinitis are common in pregnancy. The immune mechanisms underlying the effects of asthma on pregnancy and vice versa are not completely understood. The aim of this study was to investigate changes in regulatory T and B cells in asthmatic women from late pregnancy to postpartum. METHODS Four groups of women were enrolled for this study: asthmatic (n=23) and healthy (n=43) third trimester-pregnant women and asthmatic (n=33) and healthy (n=35) nonpregnant women. Pregnant women were also evaluated postpartum (>6 weeks after delivery). Blood samples were taken from each woman and flow cytometry was used to characterize circulating regulatory T cells (Tregs) and regulatory B cells (Bregs). Foxp3 expression was assessed in CD4DimCD25Hi Tregs. RESULTS Tregs did not vary significantly from pregnancy to postpartum in asthmatic or healthy women, but CD24HiCD38Hi Bregs decreased in pregnancy and increased significantly postpartum. Foxp3 expression in Tregs was also impaired during pregnancy in both asthmatic and healthy women, but recovered postpartum. Asthmatic pregnant women had higher Foxp3 expression levels than healthy pregnant women (P=.007), probably due to the use of control medication. CONCLUSIONS Women with controlled asthma showed variations in regulatory cell subsets during pregnancy and postpartum. A similar pattern was observed for Foxp3 expression and CD24HiCD38Hi Bregs during this period, corroborating the interaction between Tregs and Bregs in immune responses. Considering the immunomodulatory potential of these immune mediators, more studies are needed to evaluate their relationship with asthma and rhinitis complications in pregnancy.
A Novel Three-Phase Buck Converter with Bootstrap Driver Circuit

Analysis and design consideration of the novel three phase converter with new bootstrap driver circuit for the mobile micro processor in the laptop PC are presented. The voltage conversion ratio of the proposed converter is one third of the duty cycle. The voltage across the switches during switching operation is one-third of the input source voltage. The current ripple of the output smoothing capacitor is the same as that of conventional five-phase buck converter. The current balance of the respective phases is automatically achieved without any current sensing means. The above fine characteristics are simply achieved with two additional capacitors.
Habilidades sociales en el espectro autista

Este trabajo es de naturaleza teorica. El proposito fue identificar las caracteristicas de las habilidades sociales con las que cuenta una persona del espectro autista y hasta que punto estas pueden desarrollarse en el mismo. Se revisan los aportes de investigadores como Reviere (1997), Melendez (2009) y el DSM-IV (2002), quienes consideran al autismo como un trastorno generalizado de desarrollo de tipo neurologico que afecta tres funciones especificas rela- cionadas entre si, las cuales se desarrollan durante los tres primeros anos de su vida, estas son: la interaccion social, dificultad del lenguaje comunicativo y patrones de comportamiento, intereses y actividades restringidas repetitivas y estereotipadas. Asimismo, para la comprension de las habilidades sociales las teorias de aprendizaje social y vica- rio, las cuales indican que el individuo posee una capacidad para percibir, comprender, descifrar y, posteriormente, responder a determinados estimulos sociales en general. Se concluye que ninguna persona esta restringida a desa- rrollar estas habilidades que en definitiva son vitales para nuestra adaptacion en el contexto que sea, de la misma forma una persona perteneciente al espectro autista puede poseer y desarrollar tan igual que otra persona “normal” las habilidades sociales.
Rotation Removed Stabilization of Omnidirectional Videos Using Optical Flow

Omnidirectional cameras are often used with robots to provide an immersive view of the surroundings. However, robots often have unstable motion and undergo rotation. In this work, we formulate a method to stabilize the viewpoint of Omnidirectional videos by removing the rotation using dense optical flow fields. The method works by first projecting each Omnidirectional video frame on a unit sphere, measuring the optical flow at every point on the sphere, and finding the direction that minimizes its rotational component in a frame by frame manner. The Omnidirectional video is de-rotated and a ‘rotation-less, translation-only’ viewpoint is generated. Such a technique is well suited to work in any environment, even with sparse texture or repeating patterns where feature correspondence based methods may fail.
Pathomechanism of Loss of Elasticity and Hypertrophy of Lumbar Ligamentum Flavum in Elderly Patients With Lumbar Spinal Canal Stenosis

Study Design. A histologic, biologic, and immunohistochemical assessment using human samples of lumbar ligamentum flavum. Objective. To clarify the pathomechanism of loss of elasticity and hypertrophy of the lumbar ligamentum flavum (LF) in the elderly population. Summary of Background Data. The most common spinal disorder in elderly patients is lumbar spinal canal stenosis, causing low back and leg pain, and paresis. Canal narrowing, in part, results from hypertrophy of the LF. Although histologic and biologic literature on this topic is available, the pathomechanism of loss of elasticity and hypertrophy of the LF is still unknown. Methods. One fetus, 5 young, and 5 elderly LF were obtained for histologic study. Hematoxylin and eosin, Alcian blue, Masson Trichrome, and Elastica Van Gieson stains were performed for each LF. Nine LF were collected and were used for biologic study of real time RT-PCR to quantitatively measure mRNA expression of Type I collagen and elastin in each LF. Results. In the LF of the fetus, elastic fibers accounted for about 75% of the entire area. In the dural aspect of the LF in the young and elderly group, the ratio was also around 75%; however, the ratio of the dorsal aspect decreased with age. Almost half of the area showing loss of elastic fibers was shown to be converted to cartilaginous tissue producing Type II collagen and proteoglycan by Alcian blue and Type II collagen immunohistochemistry. The area, which did not stain black with EV nor blue with AB stain, was positively stained blue with T stain, indicating scarring. The area of the normal dural layer was 18.0 ± 2.3 and 33.8 ± 4.3 (mm2), for young and elderly group, respectively. Accordingly, it was 3.2 ± 0.8 and 18.0 ± 10.2 (mm2), for the dorsal abnormal layer. Elastin mRNA showed a relatively strong correlation (r = 0.44) with age; however, the slope was very gentle. Type I collagen mRNA showed a very strong correlation (r = 0.80) with age. The slope was steeper, and the value reached at 1000% (10-fold) around 65 years old when compared with the LF from younger patient. Elastin mRNA showed a weak correlation (r = 0.36) with thickness, and the slope was gentle. Type I collagen mRNA showed relatively strong correlation (r = 0.52) with thickness. The slope was steeper, and the line reached at 1000% (10-fold) around 6.5 (mm) when compared with a thin LF. Conclusion. Decreased elasticity of LF in the elderly is due to the loss of elastic fibers and a concomitant increase of collagenous fibers in the dorsal aspect. LF hypertrophy could be due to the thickening of the normal elastic layer as well as of the abnormal collagenous layer.
Vasopressin-independent targeting of aquaporin-2 by selective E-prostanoid receptor agonists alleviates nephrogenic diabetes insipidus

In the kidney, the actions of vasopressin on its type-2 receptor (V2R) induce increased water reabsorption alongside polyphosphorylation and membrane targeting of the water channel aquaporin-2 (AQP2). Loss-of-function mutations in the V2R cause X-linked nephrogenic diabetes insipidus. Treatment of this condition would require bypassing the V2R to increase AQP2 membrane targeting, but currently no specific pharmacological therapy is available. The present study examined specific E-prostanoid receptors for this purpose. In vitro, prostaglandin E2 (PGE2) and selective agonists for the E-prostanoid receptors EP2 (butaprost) or EP4 (CAY10580) all increased trafficking and ser-264 phosphorylation of AQP2 in Madin-Darby canine kidney cells. Only PGE2 and butaprost increased cAMP and ser-269 phosphorylation of AQP2. Ex vivo, PGE2, butaprost, or CAY10580 increased AQP2 phosphorylation in isolated cortical tubules, whereas PGE2 and butaprost selectively increased AQP2 membrane accumulation in kidney slices. In vivo, a V2R antagonist caused a severe urinary concentrating defect in rats, which was greatly alleviated by treatment with butaprost. In conclusion, EP2 and EP4 agonists increase AQP2 phosphorylation and trafficking, likely through different signaling pathways. Furthermore, EP2 selective agonists can partially compensate for a nonfunctional V2R, providing a rationale for new treatment strategies for hereditary nephrogenic diabetes insipidus.
The requirement for a 5' stem-loop structure in brome mosaic virus replication supports a new model for viral positive-strand RNA initiation

Sequences with strong similarity to internal control regions 1 and 2 (ICR1 and -2; A and B boxes) of tRNA genes are found at the 5' termini of the genomic RNAs of brome mosaic virus (BMV) and other plant viruses. The functionality of these motifs was studied by introducing point mutations into the ICR2-like sequence of pRNA-2 M/S, a BMV RNA-2 deletion mutant that replicates in the presence of RNAs-1 and -2 but does not encode a functional viral protein. The accumulation of positive-strand progeny from pRNAs bearing single and double base substitutions was 70 to 91% lower than that of the wild type, while the addition of single bases at position 8 of this motif reduced replication by 80%. These dramatic decreases in positive-strand synthesis paralleled decreases in transcription seen (C. Traboni, G. Ciliberto, and R. Cortese, Cell 36:179-187, 1984) from a tRNAPro gene containing similar mutations, suggesting comparable functions for the ICR regions in protein factor binding and demonstrating that a wild-type composition of the virus ICR2-like motif is required for proper RNA replication. Substitutions introduced at bases surrounding the ICR2 motif yielded levels of pRNA replication that differed, depending on the maintenance of a putative 5' stem-loop structure in the positive strand of the viral genome. Mutations disrupting this positive-strand stem-loop while maintaining the integrity of the complementary negative-strand structure reduced pRNA replication by 85 to 97%. In contrast, disruption of the negative-strand structure while maintaining the positive-strand stem-loop did not reduce pRNA replication. Similar positive-strand structures can be predicted to form from 5' sequences of cucumber mosaic virus (strain Q) and cowpea chlorotic mottle virus RNAs-1 and -2, supporting the concept that such structures comprise an integral part of virus genomic positive-strand promoters. The requirement of a stem-loop structure present on the positive-strand provided the basis for a new model describing how these sequence and structural elements act in the production of virus positive-strand RNA.
Executive Impairment Is Associated with Impaired Memory Performance in Working-Aged Stroke Patients

Abstract Objectives: Executive dysfunction is associated with impaired memory performance, but controversies remain about which aspects of memory are involved and how general intelligence influences these connections. We aimed to clarify these connections in stroke patients by comparing various memory measures in patients with and without executive impairment. Methods: Our consecutive cohort included patients with a first-ever ischemic stroke. Neuropsychological assessments were completed 6 months and 2 years after stroke. We classified patients as executively impaired, when at least two of five executive measures were defective at 6 months. At both 6 months and 2 years, we compared list learning of unrelated words, story recall, and recall of geometric figures in patients with and without executive impairment, while controlling for general intelligence. Results: Patients with executive impairment (n=66; 37%) performed worse in list learning (p=.001; partial η2=.058) and immediate recall of a logical passage (p=.010; partial η2=.037) 6 months after stroke compared to executively intact patients (n=113). At the end of the 2-year follow-up period, the patients who were executively impaired at 6 months (n=53; 37%) still performed worse than executively intact patients (n=92) in list learning (p<.001; partial η2=.096), and additionally in delayed recall of the list (p=.006; partial η2=.052) and immediate recall of geometric figures (p=.007; partial η2=.050). Conclusions: In our working-aged stroke patients, executive impairment was common. Executive impairment was associated with memory tasks that provided less inherent structure and required the use of active memory strategies. Clinicians should remember this role of executive dysfunction when interpreting memory performance. (JINS, 2016, 22, 1–10)
Does Socioeconomic Status Matter? Race, Class, and Residential Segregation

Spatial assimilation theory predicts that racial and ethnic residential segregation results at least in part from socioeconomic differences across groups. In contrast, the place stratification perspective emphasizes the role of prejudice and discrimination in shaping residential patterns. This article evaluates these perspectives by examining the role of race and class in explaining the residential segregation of African Americans, Hispanics, and Asians from non-Hispanic whites in all U.S. metropolitan areas over the 1990 to 2000 period. Using the dissimilarity index and various indicators of socioeconomic status (SES), we find that in both 1990 and 2000 high-SES racial and ethnic groups were significantly less segregated from non-Hispanic whites than corresponding low-SES groups, especially among Hispanics and Asians—much as the spatial assimilation model would predict. Consistent with the place stratification model, African Americans of all SES levels continued to be more segregated from whites than were Hispanics and Asians, and this changed little between 1990 and 2000. However, the importance of SES in explaining the segregation of African Americans from whites increased over the period, while not for Hispanics and Asian Americans, providing support for a modest increase in the applicability of the spatial assimilation model for African Americans in the 1990s.
Estimation of Path-Integrated Attenuation and Its Nonuniformity From TRMM/PR Range Profile Data

Range profile data from the surface echo of the Precipitation Radar (PR) onboard the Tropical Rainfall Measuring Mission (TRMM) satellite enable the assessment of the nonuniformity of rainfall. The surface echo profile can be converted to a horizontal pattern of surface echo strength within the PR's footprint at off-nadir angles. Then, using the no-rain surface echo profile over ocean as a reference, the horizontal pattern of the path-integrated attenuation (PIA) can be estimated under moderate to heavy rainfall. Based on the horizontal pattern of the PIA, the nonuniform beam-filling parameter is estimated. However, this technique is applicable only to off-nadir angles and over ocean. Comparisons using ground-based radar data obtained simultaneously with TRMM data verify the effectiveness of this technique
Non‐stereoselective reversal of neuropathic pain by naloxone and naltrexone: involvement of toll‐like receptor 4 (TLR4)

Although activated spinal cord glia contribute importantly to neuropathic pain, how nerve injury activates glia remains controversial. It has recently been proposed, on the basis of genetic approaches, that toll‐like receptor 4 (TLR4) may be a key receptor for initiating microglial activation following L5 spinal nerve injury. The present studies extend this idea pharmacologically by showing that TLR4 is key for maintaining neuropathic pain following sciatic nerve chronic constriction injury (CCI). Established neuropathic pain was reversed by intrathecally delivered TLR4 receptor antagonists derived from lipopolysaccharide. Additionally, (+)‐naltrexone, (+)‐naloxone, and (−)‐naloxone, which we show here to be TLR4 antagonists in vitro on both stably transfected HEK293‐TLR4 and microglial cell lines, suppressed neuropathic pain with complete reversal upon chronic infusion. Immunohistochemical analyses of spinal cords following chronic infusion revealed suppression of CCI‐induced microglial activation by (+)‐naloxone and (−)‐naloxone, paralleling reversal of neuropathic pain. Together, these CCI data support the conclusion that neuron‐to‐glia signaling through TLR4 is important not only for initiating neuropathic pain, as suggested previously, but also for maintaining established neuropathic pain. Furthermore, these studies suggest that the novel TLR4 antagonists (+)‐naloxone and (−)‐naloxone can each fully reverse established neuropathic pain upon multi‐day administration. This finding with (+)‐naloxone is of potential clinical relevance. This is because (+)‐naloxone is an antagonist that is inactive at the (−)‐opioid selective receptors on neurons that produce analgesia. Thus, these data suggest that (+)‐opioid antagonists such as (+)‐naloxone may be useful clinically to suppress glial activation, yet (−)‐opioid agonists suppress pain.