Miracle-dz/UniFAR-FTUs huggingface dataset:
A Method to Train Marmosets in Visual Working Memory Task and Their Performance

Learning and memory processes are similarly organized in humans and monkeys; therefore, monkeys can be ideal models for analyzing human aging processes and neurodegenerative diseases such as Alzheimer’s disease. With the development of novel gene modification methods, common marmosets (Callithrix jacchus) have been suggested as an animal model for neurodegenerative diseases. Furthermore, the common marmoset’s lifespan is relatively short, which makes it a practical animal model for aging. Working memory deficits are a prominent symptom of both dementia and aging, but no data are currently available for visual working memory in common marmosets. The delayed matching-to-sample task is a powerful tool for evaluating visual working memory in humans and monkeys; therefore, we developed a novel procedure for training common marmosets in such a task. Using visual discrimination and reversal tasks to direct the marmosets’ attention to the physical properties of visual stimuli, we successfully trained 11 out of 13 marmosets in the initial stage of the delayed matching-to-sample task and provided the first available data on visual working memory in common marmosets. We found that the marmosets required many trials to initially learn the task (median: 1316 trials), but once the task was learned, the animals needed fewer trials to learn the task with novel stimuli (476 trials or fewer, with the exception of one marmoset). The marmosets could retain visual information for up to 16 s. Our novel training procedure could enable us to use the common marmoset as a useful non-human primate model for studying visual working memory deficits in neurodegenerative diseases and aging.
Isolation and Genetic Characterization of Phenol-Utilizing Marine Bacteria and Their Phenol Degradation Pathway

Phenolic compounds are widely distributed toxic pollutants in seawater, and their effective degradation is very important for bioremediation programs. In this study, nine phenol-degrading bacteria were isolated from seawater samples, which were collected from the coastal areas of Japan. Besides the enrichment substrate phenol, all isolates could utilize at least one isomer of cresol as the sole source of carbon. A 16S rRNA gene sequence analysis indicated that all strains were affiliated with the class Gammaproteobacteria, four strains were closely related to Spongiibacter, four were closely related to Marinobacter, and one was closely related to Photobacterium. During growth on phenol, all isolates produced a yellow product, and a whole-cell study indicated that it was an extradiol meta-ring cleavage product of catechol, 2-hydroxymuconate semialdehyde. Phylogenetic analysis revealed that the partial gene encoding the largest subunit of the multicomponent phenol hydroxylase of the isolates was similar to that of terrestrial bacteria, thereby suggesting that phenol is converted into catechol by marine bacteria. We also suggest that horizontal transfer of the gene may occur not only among marine bacteria but also between the genera Marinobacter and Pseudomonas.
Exploiting Cluster-based Meta Paths for Link Prediction in Signed Networks

Many online social networks can be described by signed networks, where positive links signify friendships, trust and like; while negative links indicate enmity, distrust and dislike. Predicting the sign of the links in these networks has attracted a great deal of attentions in the areas of friendship recommendation and trust relationship prediction. Existing methods for sign prediction tend to rely on path-based features which are somehow limited to the sparsity problem of the network. In order to solve this issue, in this paper, we introduce a novel sign prediction model by exploiting cluster-based meta paths, which can take advantage of both local and global information of the input networks. First, cluster-based meta paths based features are constructed by incorporating the newly generated clusters through hierarchically clustering the input networks. Then, the logistic regression classifier is employed to train the model and predict the hidden signs of the links. Extensive experiments on Epinions and Slashdot datasets demonstrate the efficiency of our proposed method in terms of Accuracy and Coverage.
The Role of the Host Response in Periodontal Disease Progression: Implications for Future Treatment Strategies.

In this paper, we review the relevant aspects of host responses in periodontal diseases as we understand them today. Discussion will focus on neutrophil function, lymphocytes and the immune response, macrophage function, cytokines and complement, fibroblasts and growth factors, and regeneration. Recent literature and concepts will be presented with an emphasis on future directions and application to treatment regimens. J Periodontol 1993; 64:792-806.
Brief Behavioral Treatment for Insomnia in Persons Living with HIV

ABSTRACT This study examined the feasibility and preliminary efficacy of brief behavioral treatment for insomnia (BBTI) for persons living with HIV (PLWH). Of the 22 persons enrolled, 9 were lost before starting treatment, and one dropped out after starting BBTI. Acceptability was rated favorably by those completing the treatment (n = 12). The most common problems pertained to sleep hygiene: variable bedtimes and rise times, watching television, or consuming caffeine. Improvements on sleep outcomes at posttreatment were clinically and statistically significant on questionnaire and sleep diary outcomes. This study supports the overall feasibility of BBTI in PLWH, and the preliminary evidence supports further research on this treatment for PLWH who have insomnia, but dropouts indicate that some individuals may have difficulty initiating treatment.
Restoration of multilayered single-photon 3D Lidar images

This paper presents a new algorithm for the restoration of multilayered three-dimensional laser detection and ranging (3D Lidar) images. For multilayered targets such as semitransparent surfaces or when the transmitted light of the laser beam is incident on multiple surfaces at different depths, the returned signal may contain multiple peaks. Considering the Poisson statistics of these observations leads to a convex data fidelity term that is regularized using appropriate functions accounting for the spatial correlation between pixels and the sparse depth repartition of targets. More precisely, the spatial correlation is introduced using a convex total variation (TV) regularizer, and a collaborative sparse prior is used to introduce the depth prior knowledge. The resulting minimization problem is solved using the alternating direction method of multipliers (ADMM) that offers good convergence properties. The algorithm was validated using field data representing a man standing 1 meter behind camouflage, at an approximate stand-off distance of 230m from the system. The results show the benefit of the proposed strategy in that it improves the quality of the imaged objects at different depths and under reduced acquisition times.
Impact of Pre-existing Kidney Dysfunction on Outcomes Following  Transcatheter Aortic Valve Replacement

Background: Pre-existing chronic kidney disease (CKD) portends adverse outcomes following heart valve surgery. However, only limited and conflicting evidence is available on the impact of CKD on outcomes following transcatheter aortic valve replacement (TAVR). The objective of this review was to evaluate the effect of pre-existing CKD on TAVR outcomes. Methods: We performed a systematic electronic search using the PRISMA statement to identify all randomized controlled trials and observational studies investigating the effect of pre-existing CKD on outcomes following TAVR. 30-day and long-term outcomes were measured comparing patients with Glomerular filtration rate (GFR) ≥60 to those with GFR <60. Results: Ten studies were analyzed comprising of 8688 patients. Compared to patients with GFR ≥60, those with GFR < 60 had worse 30-day all cause mortality (OR 1.40, 95% CI: 1.13-1.73), cardiovascular mortality (OR 1.66, 95% CI: 1.04-2.67), strokes (OR 1.39, 95% CI: 1.05-1.85), acute kidney injury (OR 1.42, 95% CI: 1.21-1.66) and the risk for dialysis (OR 2.13, 95% CI: 1.07-4.22). There was no difference in device success (p=0.873), major or life threatening bleeds (p = 0.302), major vascular complications (p=0.525), need for pacemaker implantation (p = 0.393) or paravalvular leaks (p = 0.630). All-cause mortality at 1 year was also significantly higher in patients with GFR <60 (OR 1.80, 95% CI: 1.26-2.56). Conclusion: Pre-existing CKD defined as GFR <60 is a strong predictor of worse short and long-term outcomes following TAVR. Active measures should be taken to mitigate the postprocedure risk in these group of patients.
Comparative Study on Antimicrobial Efficiency of AgSiO2, ZnAg and Ag-Zeolite for the Application of Fishery Plastic Container

AgSiO2, ZnAg and Ag-Zeolite were investigated for antimicrobial activity using Gram-negative Pseudomonas aeruginosa, Shewanella putrefaciens and Gram-positive Clostridium, Listeria monocytogens as target microorganisms by disk diffusion and Agar plate MIC method. These bacteria are responsible for microbiological and chemical spoilage of sea food mainly and from the result we found that Silver zeolite, AgSiO2 has good antimicrobial activity for all target microorganisms except for clostridium perfringem. ZnAg has also shown good antimicrobial properties against all target microorganisms except Listeria monocytogens. Only ZnAg is capable to reduce clostridium perfringem as compare to Silver zeolite and AgSiO2.
Second-Line Antiretroviral Therapy in a Workplace and Community-Based Treatment Programme in South Africa: Determinants of Virological Outcome

Background: As antiretroviral treatment (ART) programmes in resource-limited settings mature, more patients are experiencing virological failure. Without resistance testing, deciding who should switch to second-line ART can be difficult. The consequences for second-line outcomes are unclear. In a workplace- and community-based multi-site programme, with 6-monthly virological monitoring, we describe outcomes and predictors of viral suppression on second-line, protease inhibitor-based ART. Methods: We used prospectively collected clinic data from patients commencing first-line ART between 1/1/03 and 31/12/08 to construct a study cohort of patients switched to second-line ART in the presence of a viral load (VL) ≥400 copies/ml. Predictors of VL<400 copies/ml within 15 months of switch were assessed using modified Poisson regression to estimate risk ratios. Results: 205 workplace patients (91.7% male; median age 43 yrs) and 212 community patients (38.7% male; median age 36 yrs) switched regimens. At switch compared to community patients, workplace patients had a longer duration of viraemia, higher VL, lower CD4 count, and higher reported non-adherence on first-line ART. Non-adherence was the reported reason for switching in a higher proportion of workplace patients. Following switch, 48.3% (workplace) and 72.0% (community) achieved VL<400, with non-adherence (17.9% vs. 1.4%) and virological rebound (35.6% vs. 13.2% with available measures) reported more commonly in the workplace programme. In adjusted analysis of the workplace programme, lower switch VL and younger age were associated with VL<400. In the community programme, shorter duration of viraemia, higher CD4 count and transfers into programme on ART were associated with VL<400. Conclusion: High levels of viral suppression on second-line ART can be, but are not always, achieved in multi-site treatment programmes with both individual- and programme-level factors influencing outcomes. Strategies to support both healthcare workers and patients during this switch period need to be evaluated; sub-optimal adherence, particularly in the workplace programme must be addressed.
Biocomposites Based on Bacterial Cellulose and Apple and Radish Pulp

Abstract Bacterial cellulose (BC) pellicles obtained from an Acetobacter xylinum culture were disintegrated using mechanical methods to be used as reinforcement to produce biocomposite sheets with Apple and Radish Pulp. The nanosize disintegrated BC pellicles were blended with microsize apple and radish pulp in the wet state and then hot pressed to produce paper-like sheets. Thermal analysis was carried out by Thermogravimetry Analysis (TGA). Mechanical properties were assessed by Quasistatic Tensile Tests and Dynamic Mechanical Analysis (DMA). High tensile moduli were obtained (up to 8 GPa) and a nearly linear dependence of Young's modulus on the BC volume fraction was observed. Morphological characterisation of biocomposite sheets and fracture surfaces performed by Scanning Electron Microscopy (SEM) revealed the structure of the disintegrated cellulose network and the failure mechanisms of the biocomposites.
Using X-Ray In-Line Phase-Contrast Imaging for the Investigation of Nude Mouse Hepatic Tumors

The purpose of this paper is to report the noninvasive imaging of hepatic tumors without contrast agents. Both normal tissues and tumor tissues can be detected, and tumor tissues in different stages can be classified quantitatively. We implanted BEL-7402 human hepatocellular carcinoma cells into the livers of nude mice and then imaged the livers using X-ray in-line phase-contrast imaging (ILPCI). The projection images' texture feature based on gray level co-occurrence matrix (GLCM) and dual-tree complex wavelet transforms (DTCWT) were extracted to discriminate normal tissues and tumor tissues. Different stages of hepatic tumors were classified using support vector machines (SVM). Images of livers from nude mice sacrificed 6 days after inoculation with cancer cells show diffuse distribution of the tumor tissue, but images of livers from nude mice sacrificed 9, 12, or 15 days after inoculation with cancer cells show necrotic lumps in the tumor tissue. The results of the principal component analysis (PCA) of the texture features based on GLCM of normal regions were positive, but those of tumor regions were negative. The results of PCA of the texture features based on DTCWT of normal regions were greater than those of tumor regions. The values of the texture features in low-frequency coefficient images increased monotonically with the growth of the tumors. Different stages of liver tumors can be classified using SVM, and the accuracy is 83.33%. Noninvasive and micron-scale imaging can be achieved by X-ray ILPCI. We can observe hepatic tumors and small vessels from the phase-contrast images. This new imaging approach for hepatic cancer is effective and has potential use in the early detection and classification of hepatic tumors.
Leveraging viewer comments for mood classification of music video clips

This short paper proposes a method to classify music video clips uploaded to a video sharing service into music mood categories such as 'cheerful,' 'wistful,' and 'aggressive. ' The method leverages viewer comments posted to the music video clips for the music mood classification. It extracts specific features from the comments: (1) adjectives in comments, (2) lengthened words in comments, and (3) comments in chorus sections. Our experimental results classifying 695 video clips into six mood categories showed that our method outperformed the baseline in terms of macro and micro averaged F-measures. In addition, our method outperformed the existing approaches that utilize lyrics and audio signals of songs.
Barbara McClintock’s Unsolved Chromosomal Mysteries: Parallels to Common Rearrangements and Karyotype Evolution

Two obscure studies on chromosome behavior by Barbara McClintock are revisited in light of subsequent studies and evolutionary genomics of chromosome number reduction. Two obscure studies on chromosomal behavior by Barbara McClintock are revisited in light of subsequent studies and evolutionary genomics of chromosome number reduction. The phenomenon of deficiency recovery in which adjacent genetic markers lost in the zygote reappear in later developmental sectors is discussed in light of de novo centromere formation on chromosomal fragments. Second, McClintock described a small chromosome, which she postulated carried an “X component,” that fostered specific types of chromosomal rearrangements mainly involving centromere changes and attachments to the termini of chromosomes. These findings are cast in the context of subsequent studies on centromere misdivision, the tendency of broken fragments to join chromosome ends, and the realization from genomic sequences that nested chromosomal insertion and end-to-end chromosomal fusions are common features of karyotype evolution. Together, these results suggest a synthesis that centromere breaks, inactivation, and de novo formation together with telomeres—acting under some circumstances as double-strand DNA breaks that join with others—is the underlying basis of these chromosomal phenomena.
SweepCanvas: Sketch-based 3D Prototyping on an RGB-D Image

The creation of 3D contents still remains one of the most crucial problems for the emerging applications such as 3D printing and Augmented Reality. In Augmented Reality, how to create virtual contents that seamlessly overlay with the real environment is a key problem for human-computer interaction and many subsequent applications. In this paper, we present a sketch-based interactive tool, which we term emph{SweepCanvas}, for rapid exploratory 3D modeling on top of an RGB-D image. Our aim is to offer end-users a simple yet efficient way to quickly create 3D models on an image. We develop a novel sketch-based modeling interface, which takes a pair of user strokes as input and instantly generates a curved 3D surface by sweeping one stroke along the other. A key enabler of our system is an optimization procedure that extracts pairs of spatial planes from the context to position and sweep the strokes. We demonstrate the effectiveness and power of our modeling system on various RGB-D data sets and validate the use cases via a pilot study.
A model of electrical impedance tomography implemented in nerve-cuff for neural-prosthetics control

Objective: In neural interfaces for peripheral nerve a trade-off exists between the level of invasiveness and the selectivity of neural recordings. In this study, we implement electrical impedance tomography (EIT) in a nerve cuff with the aim to investigate the achievable level of selectivity. Approach: Established modelling approaches in neural-EIT are expanded on to be used, for the first time, on myelinated fibres which are abundant in mammalian peripheral nerves and transmit motor commands. The model is then used to evaluate the viability of using EIT with a nerve cuff to record neural activity in peripheral nerves. Main results: Fibre impedance models indicate activity in unmyelinated fibres can be screened out from activity in myelinated fibres using operating frequencies above 100 Hz. At 1 kHz the transverse impedance magnitude, which is perpendicular to the fibre length axis, of inactive intra-fascicle tissue and the fraction change during neural activity are estimated to be 1142 Ω cm and −8.8 × 10−4, respectively. At 1 kHz and 10 mm spacing between the impedance measurement electrode pair, the longitudinal impedance magnitude, which is parallel to the fibre length axis, and the fraction change during neural activity are estimated to be 328 Ω cm and −0.30, respectively. We show that a novel EIT drive and measurement electrode pattern which utilises longitudinal current and longitudinal differential boundary voltage measurements could distinguish activity in different fascicles, as well as simultaneous activity in multiple fascicles, of a three-fascicle mammalian nerve using simulated data. Significance: The results of this study provide an estimate of the transient change in impedance of intra-fascicle tissue during neural activity in mammalian nerve, and present a viable EIT electrode pattern, both of which are critical steps towards implementing EIT in a nerve cuff for a recording neural interface.
FarmView : Regression Analysis of 2016 Sorghum Composition

Methods. I trained a random forest, and other regressors, on the 2016 dataset using 10-fold cross validation. I augmented the training set so there were more training samples with missingness identical to the missingness in the test set. Finally, I trained on three different views of the dataset to determine the incremental increase in predictive power from the robot-generated plus dronegenerated features, as well as the harvest phenotypes. Results The random forest regressor preformed the best with an overall r2 score of 0.436. This includes the 2.5% increase in r2 score from my missing value augmentation
The evolution of human normativity: the role of prosociality and conformity

Normative behavior is a human universal that is intimately linked to morality. Morality is an adaptation to the specifically human subsistence niche of hunting and gathering, which is skill-intensive and therefore relies on transmission of opaque knowledge and involves critical interdependence, reliance on coordinated division of labor, and synchronized collective action. This lifestyle requires the presence of a variety of emotions that coevolved with it as the proximate mechanisms enabling this adaptive function. The high-urgency feel to many of these emotions reflect their functional importance: it serves to give them priority over other motivations. It is also what, to us, and makes them recognizable as moral. The key components of human morality are (1) prosocial emotions, and (2) an urge to conform. Together, they produce the urge to comply with moral norms. Normativity is thus an integral part of human morality. It evolved when two preferences came together. Strong informational conformity, needed to enable the transmission of opaque knowledge, was already present in the anthropoid primate ancestors of hominids and hominins. The added component evolved with the evolution of strong interdependence: a strong concern for one’s reputation and fear of punishment, and thus strongly prosocial emotions. Thus, the emergence of normativity in our ancestors does not require a special explanation: it was an automatic byproduct of the emergence of moral behavior in our ancestors. Introduction An evolutionary biologist confronted with any persistent behavior, for instance food choice and diet selection, would develop the working hypothesis that it represents an adaptation molded by natural selection. The evolutionary approach, moreover, presupposes that function and mechanism fit together (Tinbergen 1963): natural selection for a particular adaptive function automatically implies selection on particular mechanisms. Thus, the presence of particular emotions must reflect the presence of evolved functions. This evolutionary approach is not necessarily incompatible with the presence of major cultural variation in this behavior (for instance, diet, processing techniques), because one major adaptive strategy is phenotypic plasticity, which in the case of behavior can be called flexibility. This flexibility is culturally supported in various primates (Whiten 2012; van Schaik 2013). In the case of food selection and diet, for instance, we see major cultural variation in food processing techniques, including technologically supported techniques (Sanz et al. 2013) and geographic variation in diet (Bastian et al. 2010).