Miracle-dz/UniFAR-FTUs huggingface dataset:
Zig-zag and replacement product graphs and LDPC codes

It is known that the expansion property of a graph influences the performance of the corresponding code when decoded using iterative algorithms. Certain graph products may be used to obtain larger expander graphs from smaller ones. In particular, the zig-zag product and replacement product may be used to construct infinite families of constant degree expander graphs. This paper investigates the use of zig-zag and replacement product graphs for the construction of codes on graphs. A modification of the zig-zag product is also introduced, which can operate on two unbalanced biregular bipartite graphs, and a proof of the expansion property of this modified zig-zag product is presented.
Role of troponin in patients with chronic kidney disease and suspected acute coronary syndrome: a systematic review.

BACKGROUND Patients with chronic kidney disease (CKD) have high prevalence of elevated serum troponin levels, which makes diagnosis of acute coronary syndrome (ACS) challenging. PURPOSE To evaluate the utility of troponin in ACS diagnosis, treatment, and prognosis among patients with CKD. DATA SOURCES MEDLINE, EMBASE, and the Cochrane Central Register of Controlled Trials through May 2014. STUDY SELECTION Studies examining elevated versus normal troponin levels in terms of their diagnostic performance in detection of ACS, effect on ACS management strategies, and prognostic value for mortality or cardiovascular events after ACS among patients with CKD. DATA EXTRACTION Paired reviewers selected articles for inclusion, extracted data, and graded strength of evidence (SOE). DATA SYNTHESIS Twenty-three studies met inclusion criteria. The sensitivity of troponin T for ACS diagnosis ranged from 71% to 100%, and specificity ranged from 31% to 86% (6 studies; low SOE). The sensitivity and specificity of troponin I ranged from 43% to 94% and from 48% to 100%, respectively (8 studies; low SOE). No studies examined how troponin levels affect management strategies. Twelve studies analyzed prognostic value. Elevated levels of troponin I or troponin T were associated with higher risk for short-term death and cardiac events (low SOE). A similar trend was observed for long-term mortality with troponin I (low SOE), but less evidence was found for long-term cardiac events for troponin I and long-term outcomes for troponin T (insufficient SOE). Patients with advanced CKD tended to have worse prognoses with elevated troponin I levels than those without them (moderate SOE). LIMITATION Studies were heterogeneous in design and in ACS definitions and adjudication methods. CONCLUSION In patients with CKD and suspected ACS, troponin levels can aid in identifying those with a poor prognosis, but the diagnostic utility is limited by varying estimates of sensitivity and specificity. PRIMARY FUNDING SOURCE Agency for Healthcare Research and Quality.
An Information Theoretic Analysis of the Temporal Synchrony Between Head Gestures and Prosodic Patterns in Spontaneous Speech

We analyze the temporal co-ordination between head gestures and prosodic patterns in spontaneous speech in a data-driven manner. For this study, we consider head motion and speech data from 24 subjects while they tell a fixed set of five stories. The head motion, captured using a motion capture system, is converted to Euler angles and translations in X, Y and Z-directions to represent head gestures. Pitch and short-time energy in voiced segments are used to represent the prosodic patterns. To capture the statistical relationship between head gestures and prosodic patterns, mutual information (MI) is computed at various delays between the two using data from 24 subjects in six native languages. The estimated MI, averaged across all subjects, is found to be maximum when the head gestures lag the prosodic patterns by 30msec. This is found to be true when subjects tell stories in English as well as in their native language. We observe a similar pattern in the root mean squared error of predicting head gestures from prosodic patterns using Gaussian mixture model. These results indicate that there could be an asynchrony between head gestures and prosody during spontaneous speech where head gestures follow the corresponding prosodic patterns.
Biometric match score fusion using RVM: A case study in multi-unit iris recognition

This paper presents a novel fusion approach to combine scores from different biometric classifiers using Relevance Vector Machine. RVM uses a combination of kernel functions on training data for classification and compared to SVM, it requires significantly reduced number of relevance vectors. The proposed RVM based fusion algorithm is evaluated using a case study on multi-unit iris recognition. Experimental results on the CASIA-Iris-V4 Thousand database show that RVM provides better accuracy compared to single unit iris recognition and existing fusion algorithms. With respect to SVM fusion, it is observed that, the accuracy of RVM and SVM are comparable, however, the time for RVM fusion is significantly reduced.
Speech Perception Benefits of Internet Versus Conventional Telephony for Hearing-Impaired Individuals

Background Telephone communication is a challenge for many hearing-impaired individuals. One important technical reason for this difficulty is the restricted frequency range (0.3–3.4 kHz) of conventional landline telephones. Internet telephony (voice over Internet protocol [VoIP]) is transmitted with a larger frequency range (0.1–8 kHz) and therefore includes more frequencies relevant to speech perception. According to a recently published, laboratory-based study, the theoretical advantage of ideal VoIP conditions over conventional telephone quality has translated into improved speech perception by hearing-impaired individuals. However, the speech perception benefits of nonideal VoIP network conditions, which may occur in daily life, have not been explored. VoIP use cannot be recommended to hearing-impaired individuals before its potential under more realistic conditions has been examined. Objective To compare realistic VoIP network conditions, under which digital data packets may be lost, with ideal conventional telephone quality with respect to their impact on speech perception by hearing-impaired individuals. Methods We assessed speech perception using standardized test material presented under simulated VoIP conditions with increasing digital data packet loss (from 0% to 20%) and compared with simulated ideal conventional telephone quality. We monaurally tested 10 adult users of cochlear implants, 10 adult users of hearing aids, and 10 normal-hearing adults in the free sound field, both in quiet and with background noise. Results Across all participant groups, mean speech perception scores using VoIP with 0%, 5%, and 10% packet loss were 15.2% (range 0%–53%), 10.6% (4%–46%), and 8.8% (7%–33%) higher, respectively, than with ideal conventional telephone quality. Speech perception did not differ between VoIP with 20% packet loss and conventional telephone quality. The maximum benefits were observed under ideal VoIP conditions without packet loss and were 36% (P = .001) for cochlear implant users, 18% (P = .002) for hearing aid users, and 53% (P = .001) for normal-hearing adults. With a packet loss of 10%, the maximum benefits were 30% (P = .002) for cochlear implant users, 6% (P = .38) for hearing aid users, and 33% (P = .002) for normal-hearing adults. Conclusions VoIP offers a speech perception benefit over conventional telephone quality, even when mild or moderate packet loss scenarios are created in the laboratory. VoIP, therefore, has the potential to significantly improve telecommunication abilities for the large community of hearing-impaired individuals.
Proteome-wide Analysis in Saccharomyces cerevisiae Identifies Several PHD Fingers as Novel Direct and Selective Binding Modules of Histone H3 Methylated at Either Lysine 4 or Lysine 36*

The PHD finger motif is a signature chromatin-associated motif that is found throughout eukaryotic proteomes. Here we have determined the histone methyl-lysine binding activity of the PHD fingers present within the Saccharomyces cerevisiae proteome. We provide evidence on the genomic scale that PHD fingers constitute a general class of effector modules for histone H3 trimethylated at lysine 4 (H3K4me3) and histone H3 trimethylated at lysine 36 (H3K36me3). Structural modeling of PHD fingers demonstrates a conserved mechanism for recognizing the trimethyl moiety and provides insight into the molecular basis of affinity for the different methyl-histone ligands. Together, our study suggests that a common function for PHD fingers is to transduce methyl-lysine events and sheds light on how a single histone modification can be linked to multiple biological outcomes.
EXPRESSION AND ACTIVITIES OF N-MYRISTOYLTRANSFERASE AND CALCINEURIN IN NORMAL AND INFLAMED LUNGS

The role of N-myristoyltransferase and calcineurin is well established in signaling pathways. However, there are no data on their expression and activities in normal and inflamed lungs. The mechanisms of lung inflammation induced following administration of lipopolysaccharides (LPS) or exposure to swine barn air remain unclear. Therefore, we examined expression and activities of N-myristoyltransferase and calcineurin in normal and inflamed lungs of rats. Histopathology showed acute inflammation in the lungs of rats exposed to barn air or LPS but not of control rats. There was no difference in the activities of N-myristoyltransferase and calcineurin among the control, barn-exposed, and LPS-treated rat lungs. Although N-myristoyltransferase and calcineurin were localized in airway epithelium, blood vessel walls, alveolar macrophages, and septa in the lungs of rats from all the groups, the staining intensity was increased in the lungs from rats exposed to intravenous LPS or barn air. Densitometric analyses of Western blots of 55- and 60-kDa polypeptide bands corresponding to N-myristoyltransferase and calcineurin, respectively, in the lung homogenates revealed no differences among the groups. These results show that expression of myristoyltransferase and calcineurin in lung epithelium and endothelium and a cell-specific increase in immunohistochemical expression.
Molecular Identification and Phylogeny of Commonly Occurring Periodontal Bacteria using 16S rRNA Gene Sequences

This study reports the detection and identification of four commonly occurring dental bacteria including Prophyromonas gingivalis , Bacteroides forsythes , Actinobacillus actinomycetenicomitans and Prevotella intermedia using PCR amplification with 16S rRNA sequence-specific primers. The phylogenetic relationship among these bacteria was also studied after retrieving 16S rRNA gene sequences from the GenBank nucleotide database. There were positive amplifications for Actinobacillus actinomycetenicomitans in 6 out of 8 samples followed by Prophyromonas gingivalis (5/8) and Bacteroides forsythes (3/8) whereas only one sample was positive for Prevotella intermedia . Multiple sequence alignment showed a large number of variable sites (547 out of post-alignment 1510 sites) while the average frequencies of conserved sequences among the species were 60.9%. The phylogenetic tree clearly differentiated Actinobacillus actinomycetenicomitans and Prevotella intermedia from Prophyromonas gingivalis and Bacteroides forsythes , the later two species belong to the same family (but different genera) and appeared as a separate clade. The hierarchical flow of the tree clearly showed the discriminatory power of 16S rRNA marker from phylum to genus level. In conclusion, PCR amplification using 16S rRNA sequence-specific primers provides a sensitive and specific method for identification of dental bacteria. This method does not require any culturing or DNA extraction hence is more simple and time saving. Post-amplification sequencing of 16S rRNA provides a reliable tool for phylogenetic and molecular diversity analyses.
SoftTRR: Protect Page Tables Against RowHammer Attacks using Software-only Target Row Refresh

Rowhammer attacks that corrupt level-1 page tables to gain kernel privilege are the most detrimental to system security and hard to mitigate. However, recently proposed software-only mitigations are not effective against such kernel privilege escalation attacks. In this paper, we propose an effective and practical software-only defense, called SoftTRR, to protect page tables from all existing rowhammer attacks on x86. The key idea of SoftTRR is to refresh the rows occupied by page tables when a suspicious rowhammer activity is detected. SoftTRR is motivated by DRAM-chip-based target row refresh (ChipTRR) but eliminates its main security limitation (i.e., ChipTRR tracks a limited number of rows and thus can be bypassed by many-sided hammer). Specifically, SoftTRR protects an unlimited number of page tables by tracking memory accesses to the rows that are in close proximity to page-table rows and refreshing the page-table rows once the tracked access count exceeds a pre-defined threshold. We implement a prototype of SoftTRR as a loadable kernel module, and evaluate its security effectiveness, performance overhead, and memory consumption. The experimental results show that SoftTRR protects page tables from real-world rowhammer attacks and incurs small performance overhead as well as memory cost.
This paper is included in the Proceedings of the 19th USENIX Symposium on Networked Systems Design and Implementation.

LoRaWAN has emerged as an appealing technology to connect IoT devices but it functions without explicit coordination among transmitters, which can lead to many packet collisions as the network scales. State-of-the-art work proposes various approaches to deal with these collisions, but most functions only in high signal-to-interference ratio (SIR) conditions and thus does not scale to real scenarios where weak receptions are easily buried by stronger receptions from nearby transmitters. In this paper, we take a fresh look at LoRa’s physical layer, revealing that its underlying linear chirp modulation fundamentally limits the capacity and scalability of concurrent LoRa transmissions. We show that by replacing linear chirps with their non-linear counterparts, we can boost the through-put of concurrent LoRa transmissions and empower the LoRa receiver to successfully receive weak transmissions in the presence of strong colliding signals. Such a non-linear chirp design further enables the receiver to demodulate fully aligned collision symbols — a case where none of the existing approaches can deal with. We implement these ideas in a holistic LoRaWAN stack based on the USRP N210 software-deﬁned radio platform. Our head-to-head comparison with two state-of-the-art research systems and a standard LoRaWAN base-line demonstrates that CurvingLoRa 1 improves the network throughput by 1.6–7.6 ⇥ while simultaneously sacriﬁcing neither power efﬁciency nor noise resilience.
One‐Hertz Waves at Mars: MAVEN Observations

We perform a survey of 1‐Hz waves at Mars utilizing Mars Atmosphere and Volatile EvolutioN (MAVEN) spacecraft observations for a Martian year. We find that the 1‐Hz wave occurrence rate shows an apparent variation caused by masking of the waves by background turbulence during the times when the background turbulence levels are high. To correct for this turbulence masking, we select waves that occur in time intervals where the background turbulence levels are low. We find that the extreme ultraviolet flux does not affect the wave occurrence rate significantly, suggesting that the newly born pickup ions originating in the Mars's exosphere contribute minimally to the 1‐Hz wave generation. We find that the wave occurrence rates are higher for low Mach numbers and low beta values than for high Mach numbers and high beta values. Further, we find that a high percentage of 1‐Hz waves satisfy the group‐standing condition, which suggests that a high percentage of the waves seen as monochromatic waves in the spacecraft frame can be broadband waves in the solar wind frame that have group velocities nearly equal and opposite to the solar wind velocity. We infer that the wave occurrence rate trends with the Mach number and proton beta are a consequence of how the Mach numbers and beta values influence the wave generation and damping or how those parameters affect the group‐standing condition. Finally, we find that the 1‐Hz waves are equally likely to be found in both the quasi‐parallel and the quasi‐perpendicular foreshock regions.
IfN / Farsi-Database : A Database of Farsi Handwritten City Names

The great success and high recognition rates of both OCR systems and recognition systems for handwritten words are inconceivable without the availability of huge data sets of real world data. For Arabic handwritten recognition systems, the availability of the IFN/ENITdatabase provides more possibilities to compare the performance of several systems, motivated by this fact we have developed a new database with the same characteristics of the IFN/ENIT-database. This make the adaptation of existing system for the Farsi handwritten words recognition easier. In this paper we present IfN/Farsidatabase, a new database of handwritten Farsi words. The database consists 7,271 binary images of 1,080 Iranian province/city names, collected from 600 writers. For each image in the database, the ground truth information including its ZIP code, sequence of characters, and numbers of characters, sub-words and dots are also available. This database is available for research and academic use.
Insulin-like growth factor II and PAX3-FKHR cooperate in the oncogenesis of rhabdomyosarcoma.

The mouse myoblast C2C12 cell line transfected singly with cDNA for Pax-3, PAX3-FKHR, or insulin-like growth factor (IGF) II or cotransfected with IGF-II plus Pax-3 or with IGF-II plus PAX3-FKHR genes showed an altered morphology, a lack of differentiation, and higher proliferation rates in vitro. On s.c. injection into nude mice, tumors grew from transfected cell lines but not from cells transfected with the empty vector. Tumors derived from IGF-II/PAX3-FKHR- and IGF-II-transfected cells grew most rapidly. Cotransfection of IGF-II plus Pax-3 induced tumors comprised highly differentiated striated muscle cells; Pax-3, PAX3-FKHR, or IGF-II transfection produced tumors at varying stages of differentiation. Tumors derived from IGF-II plus PAX3-FKHR-cotransfected cells were composed of undifferentiated cells. This was the only tumor type to infiltrate the underlying muscle. The most angiogenesis and the least apoptosis were observed in the latter tumors. These results support the hypothesis that PAX3-FKHR interacts with IGF-II to play a critical role in the oncogenesis of rhabdomyosarcoma.
Interpolatory point set surfaces—convexity and Hermite data

Point set surfaces define a (typically) manifold surface from a set of scattered points. The definition involves weighted centroids and a gradient field. The data points are interpolated if singular weight functions are used to define the centroids. While this way of deriving an interpolatory scheme appears natural, we show that it has two deficiencies: Convexity of the input is not preserved and the extension to Hermite data is numerically unstable. We present a generalization of the standard scheme that we call Hermite point set surface. It allows interpolating, given normal constraints in a stable way. It also yields an intuitive parameter for shape control and preserves convexity in most situations. The analysis of derivatives also leads to a more natural way to define normals, in case they are not supplied with the point data. We conclude by comparing to similar surface definitions.
Purification of Dunaliella salina and Effects of Associated– Bacteria on its Physiological and Biochemical Characteristics

Investigations of microalgae-bacteria relationship are important to studies of microbial ecology, red tide, aquaculture and pollutant degradation, etc. To date, microalgae-bacteria interactions are still not well understood, and purification of eukaryotic microalgae is also rarely mentioned. Here, bacteria-free Dunaliella salina was obtained with optimized antibiotic treatments. Axenic microalgal growth did not differ significantly with non-axenic algae in f /2 medium. However, when the contents of nitrogen and phosphorus were 10-fold higher of f/ 2, or there were no vitamins or trace elements in f/ 2 medium, the non-axenic algae grow much faster-increased 6.78%, 10.25% and 10.19% than axenic algal biomass, respectively. Associated bacteria haven’t significant effect on microalgal intracellular gross fat and ash contents, while improved microalgal intracellular protein and intra-and extra-cellular total carbohydrate contents during most growth stages. Associated bacteria didn’t impact algal nitrogen uptake. While under high nutrient concentration conditions, the phosphorus contents decreased more rapidly in non-axenic algal culture (decreased 40.48%) than in axenic algal culture (decreased 5.99%) within the first 4 days, suggesting that non-axenic algal phosphorus uptake was stronger. The study provided a simpler system and effective references to research of microalgae-bacteria relationship.
Matrix Metalloproteinase-2 Plays a Critical Role in the Pathogenesis of White Matter Lesions After Chronic Cerebral Hypoperfusion in Rodents

Background and Purpose— Cerebrovascular white matter (WM) lesions contribute to cognitive impairment and motor dysfunction in the elderly. A disruption of the blood–brain barrier (BBB) is believed to be a critical early event leading to these WM lesions. Previous studies have suggested the involvement of matrix metalloproteinase-2 (MMP-2) in BBB disruptions and the upregulation of MMP-2 after chronic cerebral hypoperfusion in a rat model. In the present study, we asked whether MMP-2 is involved in the BBB disruption and the subsequent WM lesions after chronic cerebral hypoperfusion. Methods— We compared the severity of white matter lesions in rats after chronic cerebral hypoperfusion with or without an MMP inhibitor. Then, we also induced the chronic cerebral hypoperfusion in wild-type and MMP-2-null mice. Results— In the rats treated with a relatively selective MMP-2 inhibitor, AG3340, the WM lesions after chronic cerebral hypoperfusion were significantly less severe, and the number of activated astroglia and microglia were also significantly lower as compared with the vehicle-treated rats. Gene knockout of MMP-2 also reduced the severity of the WM lesions and the number of activated astroglia and microglia in a mice system. In both rodents, the disruption of BBB function, as assessed by IgM staining and the Evans blue extravasation test, was less severe when MMP-2 activity was attenuated. Conclusions— These findings indicate that MMP-2 plays a critical role in the BBB disruption, glial cell activation, and WM lesions after chronic cerebral hypoperfusion and suggest the potential value of MMP-2 inhibitors as a therapeutic tool in cerebrovascular WM lesions.