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Components of transcriptional machinery are selectively partitioned into specific condensates, often mediated by protein disorder, yet we know little about how this specificity is achieved. Here, we show that condensates composed of the intrinsically disordered region (IDR) of MED1 selectively partition RNA polymerase II together with its positive allosteric regulators while excluding negative regulators. This selective compartmentalization is sufficient to activate transcription and is required for gene activation during a cell-state transition. The IDRs of partitioned proteins are necessary and sufficient for selective compartmentalization and require alternating blocks of charged amino acids. Disrupting this charge pattern prevents partitioning, whereas adding the pattern to proteins promotes partitioning with functional consequences for gene activation. IDRs with similar patterned charge blocks show similar partitioning and function. These findings demonstrate that disorder-mediated interactions can selectively compartmentalize specific functionally related proteins from a complex mixture of biomolecules, leading to regulation of a biochemical pathway.

Objectives: The objectives of the study were to determine the association of gingival biotype and secondary stability of orthodontic mini-implants using resonance frequency analysis. Materials and Methods: Twenty patients, each receiving two mini-implants, were divided into two groups; thick and thin gingival biotype based on the thickness of gingiva before mini-implant placement. Implant stability was assessed at the time of placement; at the 1st, 2nd, 3rd, and 4th month by resonance frequency analysis. Peri-implant soft-tissue conditions were also examined at each month till 4 months interval using periodontal indices. Results: Thick and thin gingival biotype groups showed statistically different implant stability quotient (ISQ). Mini-implants showing signs of failure consistently displayed lesser ISQ. Statistically significant difference was observed in the scores of peri-implant indices of failure and no failure group of mini-implants. Conclusion: Mini-implants in thin gingival biotype are more susceptible to failure and peri-implantitis compared to thick gingival biotype. Longitudinal assessment of mini-implant stability may help predict failure so as to avoid long duration and cost of orthodontic treatment.

Driven by the strong need for cheap and integrable Si-based optoelectronic devices for a wide range of applications, continuing endeavors have been made to develop structures for light emission, modulation, and detection in this material system. Here, we report the realization of room-temperature stimulated emission in the technologically crucial 1.5 micron wavelength range from Er-doped GaN/AlN multiple-quantum wells on silicon and sapphire. Employing the well-acknowledged variable stripe technique, we have demonstrated an optical gain up to 170 cm-1 in the multiple-quantum well structures. The observation of the stimulated emission is accompanied by the characteristic threshold behavior of emission intensity as a function of pump fluence, spectral linewidth narrowing and excitation length. The demonstration of room-temperature lasing at the minimum loss window of optical fibers and in the eye-safe wavelength region of 1.5 micron are highly sought-after for use in many applications including defense, industrial processing, communication, medicine, spectroscopy and imaging. As the synthesis of Er-doped GaN epitaxial layers on silicon and sapphire has been successfully demonstrated, the results laid the foundation for achieving hybrid GaN-Si lasers providing a new pathway towards full photonic integration for silicon optoelectronics.

Graphene-based photodetectors have attracted attention for realizing optoelectronic devices including photodetectors. We report a graphene field effect transistor on silicon for broadband light detection from the ultraviolet to near-infrared region, which is compatible with the silicon technology and does not need a complicated fabrication process. The photodetectors show an improved responsivity. Specifically, fabricated graphene photodetectors shows a photo-responsivity of ~980 A/W at room temperature. These results provide a promising for the development of graphene-based optoelectronic applications with the broadband photodetection from the ultraviolet to near-infrared region.

The COVID-19 pandemic has spread across the globe at an alarming rate. However, unlike any of the previous global outbreaks the availability of a large number of SARS-CoV-2 sequences provides us with a unique opportunity to understand viral evolution in real time. We analysed 1448 full-length (>29000 nt) sequences available and identified 40 single-nucleotide substitutions occurring in >1% of the genomes. Majority of the substitutions were C to T or G to A. We identify C/Gs with an upstream TTT trinucleotide motif as hotspots for mutations in the SARS-CoV-2 genome. Interestingly, three of the 40 substitutions occur within highly conserved secondary structures in the 5’ and 3’ regions of the genomic RNA that are critical for the virus life cycle. Furthermore, clustering analysis revealed unique geographical distribution of SARS-CoV-2 variants defined by their mutation profile. Of note, we observed several co-occurring mutations that almost never occur individually. We define five mutually exclusive lineages (A1, B1, C1, D1 and E1) of SARS-CoV-2 which account for about three quarters of the genomes analysed. We identify lineage-defining leading mutations in the SARS-CoV-2 genome which precede the occurrence of sub-lineage defining trailing mutations. The identification of mutually exclusive lineage-defining mutations with geographically restricted patterns of distribution has potential implications for diagnosis, pathogenesis and vaccine design. Our work provides novel insights on the temporal evolution of SARS-CoV-2.ImportanceThe SARS-CoV-2 / COVID-19 pandemic has spread far and wide with high infectivity. However, the severeness of the infection as well as the mortality rates differ greatly across different geographic areas. Here we report high frequency mutations in the SARS-CoV-2 genomes which show the presence of linage-defining, leading and trailing mutations. Moreover, we propose for the first time, five mutually exclusive clusters of SARS-CoV-2 which account for 75% of the genomes analysed. This will have implications in diagnosis, pathogenesis and vaccine design

We are currently witnessing a major epidemic caused by the 2019 novel coronavirus (2019-nCoV). The evolution of 2019-nCoV remains elusive. We found 4 insertions in the spike glycoprotein (S) which are unique to the 2019-nCoV and are not present in other coronaviruses. Importantly, amino acid residues in all the 4 inserts have identity or similarity to those in the HIV-1 gp120 or HIV-1 Gag. Interestingly, despite the inserts being discontinuous on the primary amino acid sequence, 3D-modelling of the 2019-nCoV suggests that they converge to constitute the receptor binding site. The finding of 4 unique inserts in the 2019-nCoV, all of which have identity /similarity to amino acid residues in key structural proteins of HIV-1 is unlikely to be fortuitous in nature. This work provides yet unknown insights on 2019-nCoV and sheds light on the evolution and pathogenicity of this virus with important implications for diagnosis of this virus.

Parkinson's disease is characterized by the presence of insoluble and neurotoxic aggregates (amyloid fibrils) of an intrinsically disordered protein α-synuclein. In this study we have examined the effects of four naturally occurring polyphenols in combination with β-cyclodextrin (β-CD) on the aggregation of α-synuclein in the presence of macromolecular crowding agents. Our results reveal that even at sub-stoichiometric concentrations of the individual components, the polyphenol-β-CD combination(s) not only inhibited the aggregation of the proteins but was also effective in disaggregating preformed fibrils. Curcumin was found to be the most efficient, followed by baicalein with (-)-epigallocatechin gallate and resveratrol coming in next, the latter two exhibiting very similar effects. Our results suggest that the efficiency of curcumin results from a balanced composition of the phenolic OH groups, benzene rings and flexibility. The latter ensures proper positioning of the functional groups to maximize the underlying interactions with both the monomeric form of α-synuclein and its aggregates. The uniqueness of β-CD was reinforced by the observation that none of the other cyclodextrin variants [α-CD and HP-β-CD] used was as effective, in spite of these possessing better water solubility. Moreover, the fact that the combinations remained effective under conditions of macromolecular crowding suggests that these have the potential to be developed into viable drug compositions in the near future. MTT assays on cell viability independently confirmed this hypothesis wherein these combinations (and the polyphenols alone too) appreciably impeded the toxicity of the prefibrillar α-synuclein aggregates on the mouse neuroblastoma cell lines (N2a cells).

Amyloid assemblies are stabilized through inter-molecular H-bonding with initial structural organizations governed by extensive hydrophobic and π-stacking interactions. Apparently, the structural integrity and stability of DNA duplexes are also governed by a cooperative balance of similar interactions. Structural perturbations in both amyloids and DNA by planar molecules or intercalators essentially rely on their ability to interfere with this balance. However, poor information on amyloid interference mechanisms by intercalators has subjected researchers to undertake random trials with such anti-amyloidogenic agents. Here, we employed four different classes of DNA intercalators to investigate if their non-native, hetero-aromatic associations could modulate the amyloid aggregation pathway. We utilized micro-second scale MD simulations using the steric-zipper structure of the diabetes associated amylin fragment to identify such associations and their plausible role in subjugating higher order assemblies. The simulation estimates were experimentally validated and extended to other disease-associated amyloid systems including gelsolin, prion and lysozyme. We find that the intercalators essentially stabilize monomeric and prefibrillar assemblies, reducing their ability to transform into structured supramolecular structures. Our results conclusively establish the dominant role of aromatic-associations in diverting the course of the amyloid assembly process at the expense of stabilizing H-bonding networks. Overall this report presents comprehensive experimental and theoretical insights on the regulation of amyloidogenesis by aromatic planar moieties.

Graphene-based photodetectors have attracted strong interest for realizing optoelectronic devices, including photodetectors. Here we report a simple fabrication of graphene-germanium quantum dots for broadband light detection from visible to infrared region. The photodetectors show an improved responsivity and response speed. Specifically, the fabricated germanium quantum dots on graphene photodetector shows a responsivity of 1,500 A/W at room temperature and the response time is as fast as ~ 1 ms. These results address key challenges for broadband photodetectors from visible to infrared region, and are promising for the development of graphene-based optoelectronic applications.

Cellular prion protein (PrP) misfolds into an aberrant and infectious scrapie form (PrPSc) that lead to fatal transmissible spongiform encephalopathies (TSEs). Association of prions with G-quadruplex (GQ) forming nucleic acid motifs has been reported, but implications of these interactions remain elusive. Herein, we show that the promoter region of the human prion gene (PRNP) contains two putative GQ motifs (Q1 and Q2) that assume stable, hybrid, intra-molecular quadruplex structures and bind with high affinity to PrP. Here, we investigate the ability of PrP to bind to the quadruplexes in its own promoter. We used a battery of techniques including SPR, NMR, CD, MD simulations and cell culture-based reporter assays. Our results show that PrP auto-regulates its expression by binding and resolving the GQs present in its own promoter. Furthermore, we map this resolvase-like activity to the N-terminal region (residues 23-89) of PrP. Our findings highlight a positive transcriptional-translational feedback regulation of the PRNP gene by PrP through dynamic unwinding of GQs in its promoter. Taken together, our results shed light on a yet unknown mechanism of regulation of the PRNP gene. This work provides the necessary framework for a plethora of studies on understanding the regulation of PrP levels and its implications in prion pathogenesis.

Background Postoperative suction drains are used after total knee arthroplasty to avoid intra-articular hematoma formation although they can increase blood loss due to a negative suction effect. The use of tranexamic acid to reduce blood loss may nullify this. The aim of this study was to compare outcomes in patients undergoing total knee arthroplasty with or without drains and to analyze whether the drain's diameter also has an impact. Methods This is a prospective randomized study of patients undergoing unilateral total knee arthroplasty performed by a single surgeon. The study population was divided into three groups (A, 10G drain; B, 12G drain; and C, no drain). Pain, blood loss, swelling, wound-related complications, functional outcomes and questionnaire-based outcomes were assessed postoperatively. Results Each group had 35 patients comparable in most demographic and pre- and intraoperative characteristics. During the first 6 hours postoperatively, opioid consumption was significantly higher when the drain was not used (p = 0.036). At 3 months postoperatively, new Knee Society Score (NKSS) was highest with the use of 12G drain (p = 0.018). However, NKSS at 1 year was comparable across the three groups. With the use of tranexamic acid, blood loss and incidence of soakage of dressing were unaffected by the presence or absence of a drain. The calf girth, suprapatellar girth, soakage of dressing and range of motion were comparable in all three groups. There was no incidence of surgical site infection or deep vein thrombosis. Conclusions Presence of a suction drain significantly reduces opioid consumption during the first 6 hours after total knee arthroplasty. Use of a drain made no difference to the functional outcome at 1 year postoperatively. With the use of tranexamic acid in total knee arthroplasty, the total blood loss and the requirement of blood transfusion were unaffected by the presence or absence of closed suction drainage or by the bore of the drain used. The clinical parameters such as swelling, range of motion, infection and deep vein thrombosis also remained the same.

Ulnar nerve compression at guyon’s canal is rare and very few cases have been reported in literature. It can be missed due to its rarity. Symptoms vary from pain and paresthesia to wasting and significant loss of muscle strength, with significant deformities of the hand. The diagnosis is made by detailed history and examination, electromyography, nerve conduction velocity test, ultrasound and magnetic resonance imaging. Early decompression of nerve is treatment of choice. Here we are presenting a case of compression of ulnar nerve in guyon’s canal due to ganglionic cyst.

The identification of the Toll receptor in Drosophila was a major discovery which restructured the paradigm in immunityas well as developmental biology . Toll homologues are present in mammals where they regulate only immunity . However ,in flies, same Toll pathway controls two disparate biological processes like embryonic dorso-ventral patterning and humoralimmune response. Toll activation by Spatzle is preceded by a proteolytic cascade which is dif ferently regulated in immunityand embryonic development. Signalling downstream to Toll is similar in both processes and eventually leads to theactivation of Drosophila homologues of NF-κB proteins; Dorsal and DIF. Toll pathway, in the early embryo results ingraded expression of Dorsal protein leading to Dorso-V entral axis patterning. On the other hand, activation of Toll-Dorsalpathway in the fat-body leads to induction of antibacterial proteins in larval and adult stages. Here, we review the currentstatus of our knowledge of Dorsal pathway in embryonic development and immunity with special emphasis to regulationof target gene/s of the two pathways by Dorsal.Key W ords : Dorsal; Toll; DNA Geometr y; Dorso-Ventral Patterning; Insect Immunity

The last couple of years have seen a growing momentum toward using the Internet for conducting business. Web-based electronic commerce applications are one of the fastest growing segments of the Internet today. A key enabler for e-commerce applications is the ability to setup secure private channels over a public network. The Secure Sockets Layer protocol provides this capability and is the most widely used security protocol in the Internet. We take a close look at the working principles behind SSL with an eye on performance. We benchmark two of the popular Web servers in wide use in a number of large e-commerce sites. Our results show that the overheads due to SSL can make Web servers slower by a couple of orders of magnitude. We investigate the reason for this deficiency by instrumenting the SSL protocol stack with a detailed profiling of the protocol processing components. In light of our observations, we outline architectural guidelines for large e-commerce sites.

We provide a formal model for the Change Management process for Enterprise IT systems, and develop change scheduling algorithms that seek to attain the "change capacity" of the system. The change management process handles critical updates in the system that often use overlapping sets of servers, resulting in scheduling conflicts between the corresponding change classes. Furthermore, applications are typically associated with certain permissible downtime windows, which impose constraints on the timing of the change executions. Scheduling of changes for such systems represent a complex dynamic optimization question. In a limiting fluid regime, where changes are assumed nonatomic, we develop a scheduling policy that provably attains the change capacity of the system. We then propose and evaluate an atomic approximation of the optimal fluid scheduling policy, which is well suited for application to a real change management system. Simulation results demonstrate that the expected change execution delay and the capacity attained by the approximate policy is close to the best attainable values, when unavoidable capacity losses due to fragmentation effects are taken into account and is significantly better than a randomized scheduling policy.

In this paper, we consider the change management process for enterprise IT services with the goal of improving the efficiency of this process, i.e., minimizing change completion time and maximizing the "change capacity". The change management process handles critical updates in the system that must be implemented by a set of executing personnel. In presence of such timing constraints and scheduling conflicts between change classes, we argue that addressing the application change management question optimally involves computing solutions to NP-hard problems. Using appropriate simulation models, we evaluate various batched scheduling alternatives to understand the effect of simple process re-engineering on the change completion time, and the change capacity of the system. In addition, we examine the benefit of executor cross-training and degree of conflicts on the performance of the system. Our results indicate that a simple longest queue based scheduling approach works well in a wide range of practical scenarios. Based on these results, we recommend process re-engineering based on longest queue based scheduling with a small degree of executor cross-training.

Ethanol injection is widely used in liposome preparation. However, the parameters determining particle size distribution of the liposomal preparation has not been fully defined.A syringe pump-driven microfluidic injection device was used to produce liposomes under different conditions.Particle size of the liposomes was decreased with decrease in needle diameter (or increase in hydrodynamic pressure), decrease in lipid concentration in the alcohol solution, decrease in phase transition temperature (T(m)) of the lipid bilayer and the absence of cholesterol (or decrease in, membrane rigidity).The device used is simple to adopt and can be used for affordable production of liposomes with tunable particle size.

Publisher Summary This chapter presents the design, implementation, and initial performance evaluation of a hybrid performance modeling framework called Countach, which faithfully and efficiently captures application behavior while predicting system performance. After a small manual step of replacing hardware interactions in the system software with simulated events, a set of automated postprocessing steps converts an application to a processor model that captures memory performance and enforces tight time synchronization with the simulator. Multiple processors or hardware execution contexts can be modeled in this framework. Actual workload generators can be used unmodified to drive the performance analysis. Countach models various kinds of network servers that utilize network-processor-based network interfaces. It is a very useful tool, because it allows users to experiment with the entire spectrum of design choices, including hardware design, a rich variety of operating system optimizations, and choices of function split between the host and the network processors.

As more business applications have become web enabled, the web server architecture has evolved to provide performance isolation, service differentiation, and QoS guarantees. Various server mechanisms that provide QoS extensions, however, rely on external administrators to set the right parameter values for their desirable performance. Due to the complexity of handling varying workloads and bursty traffic, configuring such parameters optimally becomes a challenge. In this paper, we describe an observation-based approach for self-managing web servers that can adapt to changing workloads while maintaining the QoS requirements of different classes. In this approach, the system state is monitored continuously and parameter values of various system resources-primarily the accept queue and the CPU-are adjusted to maintain the system-wide QoS goals. We implement our techniques using the Apache web server and the Linux operating system. We first demonstrate the need to manage different resources in the system depending on the workload characteristics. We then experimentally demonstrate that our observation-based system monitors such as workload changes and adjusts the resource parameters of the accept queue and CPU schedulers in order to maintain the QoS requirements of the different classes.

The exponential growth in Internet traffic has motivated the development of a new breed of microprocessors called network processors, which are designed to address the performance problems resulting from the explosion in Internet traffic. The development efforts of these network processors concentrate almost exclusively on streamlining their data paths to speed up network packet processing, which mainly consists of routing and data movement. Rather than blindly pushing the performance of packet processing hardware, an alternative approach is to avoid repeated computation by applying the time-tested architecture idea of caching to network packet processing. Because the data streams presented to network processors and general-purpose CPUs exhibit different characteristics, detailed cache design tradeoffs for the two also differ considerably. This research focuses on cache memory design specifically for network processors. Using a trace-drive simulation methodology, we evaluate a series of three progressively more aggressive routing-table cache designs. Our simulation results demonstrate that the incorporation of hardware caches into network processors, when combined with efficient caching algorithms, can significantly improve the overall packet forwarding performance due to a sufficiently high degree of temporal locality in the network packet streams. Moreover, different cache designs can result in up to a factor of 5 difference in the average routing table lookup time, and thus in the packet forwarding rate.

Suez is a high-performance real-time packet router that supports fast best-effort packet routing and scalable QoS-guaranteed packet scheduling, and is built on a hardware platform consisting of a cluster of commodity PCs connected by a gigabit/sec system area network. The major goal of the Suez project is to demonstrate that the PC cluster architecture can be as cost-effective a platform for high-performance network packet routing as for parallel computing. Suez features a cache-conscious routing-table search algorithm that exploits CPU caching hardware for fast lookup by treating IP addresses directly as virtual addresses. To scale the number of real-time connections supportable with the link speed, Suez implements a fixed-granularity fluid fair queuing (FGFFQ) algorithm that completely eliminates the per-packet sorting overhead associated with conventional weighted fair queuing algorithms. This paper presents the architectural features of Suez, and reports the performance measurements of the Linux-based Suez prototype, which is built on four Pentium-II 400 MHz machines and Myrinet.