Miracle-dz/UniFAR-FTUs huggingface dataset:
Unexpected Role of α-Fetoprotein in Spermatogenesis

Background Heat shock severely affects sperm production (spermatogenesis) and results in a rapid loss of haploid germ cells, or in other words, sperm formation (spermiogenesis) is inhibited. However, the mechanisms behind the effects of heat shock on spermatogenesis are obscure. Methodology/Principal Findings To identify the inhibitory factor of spermiogenesis, experimental cryptorchid (EC) mice were used in this study. Here we show that α-fetoprotein (AFP) is specifically expressed in the testes of EC mice by proteome analysis. AFP was also specifically localized spermatocytes by immunohistochemical analysis and was secreted into the circulation system of EC mice by immunoblot analysis. Since spermatogenesis of an advanced mammal cannot be reproduced with in vitro, we performed the microinjection of AFP into the seminiferous tubules of normal mice to determine whether AFP inhibits spermiogenesis in vivo. AFP was directly responsible for the block in spermiogenesis of normal mice. To investigate whether AFP inhibits cell differentiation in other models, using EC mice we performed a partial hepatectomy (PH) that triggers a rapid regenerative response in the remnant liver tissue. We also found that liver regeneration is inhibited in EC mice with PH. The result suggests that AFP released into the blood of EC mice regulates liver regeneration by inhibiting the cell division of hepatocytes. Conclusions/Significance AFP is a well-known cancer-specific marker, but AFP has no known function in healthy human beings. Our findings indicate that AFP expressed under EC conditions plays a role as a regulatory factor in spermatogenesis and in hepatic generation.
Ultrasharp and high aspect ratio carbon nanotube atomic force microscopy probes for enhanced surface potential imaging

The resolution of scanning surface potential microscopy (SSPM) is mainly limited by non-local electrostatic interactions due to the finite probe size. Here we present high resolution surface potential imaging with ultrasharp and high aspect ratio carbon nanotube (CNT) atomic force microscopy (AFM) probes fabricated via dielectrophoresis. Enhancement of surface potential contrast by several factors is reported for integrated circuit structures and purple membrane fragments for these CNT AFM probes as compared to conventional probes. In particular, ultrahigh lateral resolution (∼2 nm) surface potential images of self-assembled bacteriorhodopsin proteins are reported at ambient conditions, with the implication of label-free protein detection by SSPM techniques.
Local perinuclear calcium signals associated with mitosis-entry in early sea urchin embryos

Using calcium-sensitive dyes together with their dextran conjugates and confocal microscopy, we have looked for evidence of localized calcium signaling in the region of the nucleus before entry into mitosis, using the sea urchin egg first mitotic cell cycle as a model. Global calcium transients that appear to originate from the nuclear area are often observed just before nuclear envelope breakdown (NEB). In the absence of global increases in calcium, confocal microscopy using Calcium Green- 1 dextran indicator dye revealed localized calcium transients in the perinuclear region. We have also used a photoinactivatable calcium chelator, nitrophenyl EGTA (NP-EGTA), to test whether the chelator- induced block of mitosis entry can be reversed after inactivation of the chelator. Cells arrested before NEB by injection of NP-EGTA resume the cell cycle after flash photolysis of the chelator. Photolysis of chelator triggers calcium release. TreatmenT with caFfeine to enhance calcium-induced calcium release increases the amplitude of NEB- associated calcium transients. These results indicate that calcium increases local to the nucleus are required to trigger entry into mitosis. Local calcium transients arise in the perinuclear region and can spread from this region into the cytoplasm. Thus, cell cycle calcium signals are generated by the perinuclear mitotic machinery in early sea urchin embryos.
The time has come to make cervical cancer prevention an essential part of comprehensive sexual and reproductive health services for HIV-positive women in low-income countries

HIV and cervical cancer are intersecting epidemics that disproportionately affect one of the most vulnerable populations in the world: women in low‐ and middle‐income countries (LMICs). Historically, the disparity in cervical cancer risk for women in LMICs has been due to the lack of organized screening and prevention programmes. In recent years, this risk has been augmented by the severity of the HIV epidemic in LMICs. HIV‐positive women are at increased risk for developing cervical precancer and cancer, and while the introduction of antiretroviral therapy has dramatically improved life expectancies among HIV‐positive women it has not been shown to improve cancer‐related outcomes. Therefore, an increasing number of HIV‐positive women are living in LMICs with limited or no access to cervical cancer screening programmes. In this commentary, we describe the gaps in cervical cancer prevention, the state of evidence for integrating cervical cancer prevention into HIV programmes and future directions for programme implementation and research.
Join Bayes Nets: A new type of Bayes net for relational data

Many real-world data are maintained in relational format, with different tables storing information about entities and their links or relationships. The structure (schema) of the database is essentially that of a logical language, with variables ranging over individual entities and predicates for relationships and attributes. Our work combines the graphical structure of Bayes nets with the logical structure of relational databases to achieve knowledge discovery in databases. We introduce Join Bayes nets, a new type of Bayes nets for representing and learning class-level dependencies between attributes from the same table and from different tables; such dependencies are important for policy making and strategic planning. Focusing on class-level dependencies brings advantages in terms of the simplicity of the model and the tractability of inference and learning. As usual with Bayes nets, the graphical structure supports efficient inference and reasoning. We show that applying standard Bayes net inference algorithms to the learned models provides fast and accurate probability estimates for queries that involve attributes and relationships from multiple tables.
Modern carbonate microbialites from an asbestos open pit pond, Yukon, Canada

Microbialites were discovered in an open pit pond at an abandoned asbestos mine near Clinton Creek, Yukon, Canada. These microbialites are extremely young and presumably began forming soon after the mine closed in 1978. Detailed characterization of the periphyton and microbialites using light and scanning electron microscopy was coupled with mineralogical and isotopic analyses to investigate the mechanisms by which these microbialites formed. The microbialites are columnar in form (cm scale), have an internal spherulitic fabric (mm scale), and are mostly made of aragonite, which is supersaturated in the subsaline pond water. Initial precipitation is seen as acicular aragonite crystals nucleating onto microbial biomass and detrital particles. Continued precipitation entombs benthic diatoms (e.g. Brachysira vitrea), filamentous algae (e.g. Oedogonium sp.), dinoflagellates, and cyanobacteria. The presence of phototrophs at spherulite centers strongly suggests that these microbes play an important initial role in aragonite precipitation. Substantial growth of individual spherulites occurs abiotically through periodic precipitation of aragonite that forms concentric laminations around spherulite centers while pauses in spherulite growth allow for colonization by microbes. Aragonite associated with biomass (δ13C = −4.6‰ VPDB) showed a 13C‐enrichment of 0.8‰ relative to aragonite exhibiting no biomass (δ13C = −5.4‰ VPDB), which suggests a modest removal of isotopically light dissolved inorganic carbon by phototrophs. The combination of a low sedimentation rate, high calcification rate, and low microbial growth rate appears to result in the formation of these microbialites. The formation of microbialites at an historic mine site demonstrates that an anthropogenically constructed environment can foster microbial carbonate formation.
Assembly of the Human Origin Recognition Complex*

The six-subunit origin recognition complex (ORC) was originally identified in the yeastSaccharomyces cerevisiae. Yeast ORC binds specifically to origins of replication and serves as a platform for the assembly of additional initiation factors, such as Cdc6 and the Mcm proteins. Human homologues of all six ORC subunits have been identified by sequence similarity to their yeast counterparts, but little is known about the biochemical characteristics of human ORC (HsORC). We have extracted HsORC from HeLa cell chromatin and probed its subunit composition using specific antibodies. The endogenous HsORC, identified in these experiments, contained homologues of Orc1-Orc5 but lacked a putative homologue of Orc6. By expressing HsORC subunits in insect cells using the baculovirus system, we were able to identify a complex containing all six subunits. To explore the subunit-subunit interactions that are required for the assembly of HsORC, we carried out extensive co-immunoprecipitation experiments with recombinant ORC subunits expressed in different combinations. These studies revealed the following binary interactions: HsOrc2-HsOrc3, HsOrc2-HsOrc4, HsOrc3-HsOrc4, HsOrc2-HsOrc6, and HsOrc3-HsOrc6. HsOrc5 did not form stable binary complexes with any other HsORC subunit but interacted with sub-complexes containing any two of subunits HsOrc2, HsOrc3, or HsOrc4. Complex formation by HsOrc1 required the presence of HsOrc2, HsOrc3, HsOrc4, and HsOrc5 subunits. These results suggest that the subunits HsOrc2, HsOrc3, and HsOrc4 form a core upon which the ordered assembly of HsOrc5 and HsOrc1 takes place. The characterization of HsORC should facilitate the identification of human origins of DNA replication.
International Conference on Computational Science , ICCS 2013 An Empirical Evaluation of the Cost and E ff ectiveness of Structural Testing Criteria for Concurrent Programs

Concurrent program testing is not a trivial task. Features like nondeterminism, communication and synchronization impose new challenges that must be considered during the testing activity. Some initiatives have proposed testing approaches for concurrent programs, in which different paradigms and programming languages are considered. However, in general, these contributions do not present a well-formed experimental study to validate their ideas. The problem is that the data used and generated during the validation is not always available, hampering the replication of studies in the context of other testing approaches. This paper presents an experimental study, taking into account the concepts of the Experimental Software Engineering to evaluate the cost, effectiveness and strength of the structural testing criteria for message-passing programs. The evaluation was conducted considering a benchmark composed of eight MPI programs. A set of eight structural testing criteria defined for message-passing programs was evaluated with the ValiMPI testing tool, which provides the support required to apply the investigated testing criteria. The results indicate the complementary aspect of the criteria and the information about cost and effectiveness has contributed to the establishment of an incremental testing strategy to apply the criteria. All material generated during the experimental study is available for further comparisons.
Biobanks and personalized medicine

We provide a mini‐review of how biobanks can support clinical genetics in the era of personalized medicine. We discuss types of biobanks, including disease specific and general biobanks not focused on one disease. We present considerations in setting up a biobank, including consenting and governance, biospecimens, risk factor and related data, informatics, and linkage to electronic health records for phenotyping. We also discuss the uses of biobanks and ongoing considerations, including genotype‐driven recruitment, investigations of gene–environment associations, and the re‐use of data generated from studies. Finally, we present a brief discussion of some of the unresolved issues, such as return of research results and sustaining biobanks over time. In summary, carefully designed biobanks can provide critical research and infrastructure support for clinical genetics in the era of personalized medicine.
Early versus delayed decompression in acute subaxial cervical spinal cord injury: A prospective outcome study at a Level I trauma center from India

Aims: This study was done with the aim to compare the clinical outcome and patients’ quality of life between early versus delayed surgically treated patients of acute subaxial cervical spinal cord injury. The current study was based on the hypothesis that early surgical decompression and fixations in acute subaxial cervical spinal cord trauma is safe and is associated with improved outcome as compared to delayed surgical decompression. Materials and Methods: A total of 69 patients were recruited and divided into early decompression surgery Group A (operated within 48 h of trauma; n = 23) and late/delayed decompression surgery Group B (operated between 48 h and 7 days of trauma; n = 46). The patients in both groups were followed up, and comparative differences noted in the neurological outcome, quality of life, and bony fusion. Results: The early surgery group spent lesser days in the intensive care unit and hospital (Group A 28.6 vs. Group B 35 days) had lesser postoperative complications (Group A 43% vs. Group B 61%) and a reduced mortality (Group A 30% vs. Group B 45%). In Group A, 38% patients had 1 American Spinal Injury Association (ASIA) grade improvement while 31% experienced >2 ASIA grade improvement. In Group B, the neurological improvement was 27% and 32%, respectively (P = 0.7). There was a significant improvement in the postoperative quality of life scores in both groups. Conclusion: Early surgery in patients with acute subaxial cervical spine injury should be considered strongly in view of the lesser complications, early discharge, and reduced mortality.
Isolation and Characterization of a Novel Strain of Mesenchymal Stem Cells from Mouse Umbilical Cord: Potential Application in Cell-Based Therapy

Human umbilical cord-derived mesenchymal stem cells (hUC-MSCs) have recently been recognized as a potential source for cell-based therapy in various preclinical animal models, such as Parkinson’s disease, cerebral ischemia, spinal cord injury, and liver failure; however, the precise cellular and molecular mechanisms underlying the beneficial outcomes remain under investigation. There is a growing concern regarding rejection and alteration of genetic code using this xenotransplantation approach. In this study, a novel strain of murine MSCs derived from the umbilical cord of wild-type and green fluorescent protein (GFP) transgenic mice have been successfully isolated, expanded, and characterized. After 10 passages, the mUC-MSCs developed a rather homogeneous, triangular, spindle-shaped morphology, and were sub-cultured up to 7 months (over 50 passages) without overt changes in morphology and doubling time. Cell surface markers are quite similar to MSCs isolated from other tissue origins as well as hUC-MSCs. These mUC-MSCs can differentiate into osteoblasts, adipocytes, neurons, and astrocytes in vitro, as well as hematopoietic lineage cells in vivo. mUC-MSCs also possess therapeutic potential against two disease models, focal ischemic stroke induced by middle cerebral artery occlusion (MCAo) and acute hepatic failure. Subtle differences in the expression of cytokine-related genes exist between mUC-MSCs and hUC-MSCs, which may retard and jeopardize the advance of cell therapy. Allografts of these newly established mUC-MSCs into various mouse disease models may deepen our insights into the development of more effective cell therapy regimens.
An infrastructure for a traffic warning system

The LIWAS traffic warning system aims at providing early warning to vehicles about road conditions, such as whether the road is slippery. The LIWAS system is currently being developed and consists of two main parts: sensors for determining the state of the road and a communication infrastructure supporting inter-vehicle communication. This paper presents our results on requirements identification, design, and prototyping of the infrastructure. The infrastructure combines communication via mobile phones with communication based on the principles of ad-hoc networking, and it supports units in being updated during operation. The presented prototypes and associated experimental results demonstrate the main functionalities of the communication infrastructure, and have led to the initial deployment of LIWAS units.
Inhibition of monocyte adhesion on brain‐derived endothelial cells by NF‐kappaB decoy/polyethylenimine complexes

The nuclear factor (NF)‐κB plays a key role in inflammatory reactions of the endothelium by controlling the expression of surface‐adhesion molecules and other inflammatory mediators, which facilitate the attachment of monocytes and lymphocytes to the endothelial surface. We investigated the inhibition of monocyte adhesion by NF‐κB transcription factor decoys complexed with polyethylenimines (PEIs) of different molecular weights and structures (800, 25, and 2.7 kDa PEI).
Same Queries, Different Data: Can We Predict Runtime Performance?

We consider MapReduce workloads that are produced by analytics applications. In contrast to ad hoc query workloads, analytics applications are comprised of fixed data flows that are run over newly arriving data sets or on different portions of an existing data set. Examples of such workloads include document analysis/indexing, social media analytics, and ETL (Extract Transform Load). Motivated by these workloads, we propose a technique that predicts the runtime performance for a fixed set of queries running over varying input data sets. Our prediction technique splits each query into several segments where each segment's performance is estimated using machine learning models. These per-segment estimates are plugged into a global analytical model to predict the overall query runtime. Our approach uses minimal statistics about the input data sets (e.g., tuple size, cardinality), which are complemented with historical information about prior query executions (e.g., execution time). We analyze the accuracy of predictions for several segment granularities on both standard analytical benchmarks such as TPC-DS [17], and on several real workloads. We obtain less than 25% prediction errors for 90% of predictions.
Specific recognition of four-way DNA junctions by the C-terminal zinc-binding domain of HPV oncoprotein E6.

E6 is an oncoprotein implicated in cervical cancers produced by " high risk " human papillomaviruses. E6 binds specifically to several cellular proteins, including the tumour suppressor p53 and the ubiquitin ligase E6-AP. However, E6 is also a DNA-binding protein which recognizes a structural motive present in four-way junctions. Here, we demonstrate that the C-terminal zinc-binding domain of E6, expressed separately from the rest of the protein, fully retains the selective four-way junction recognition activity. The domain can bind to two identical and independent sites on a single junction, whereas full-length E6 can only bind to one site. The junction bound to either one or two domains adopts an extended square conformation. These results allow us to assign the structure-dependent DNA recognition activity of E6 to its C-terminal domain, which therefore represents a new class of zinc-stabilized DNA-binding module. Comparison with the binding characteristics of other junction-specific proteins enlightens the rules which govern protein-induced deformation of four-way DNA junctions.
Visual representations embodying spacetime structure

If one defines a visual front-end to be that part of a visual system in which the structure of the optical world is represented in some least committed form, then it is plausible to assert that it reflects the structural properties, notably symmetries, of the optical environment. We propose a methodology for constructing receptive field assemblies consistent with these symmetries, which contributes to our understanding of the visual front-end in a predictive and retrodictive way.
Estimation of premorbid intelligence in traumatic brain injury : NART and AUSNART performance in an Australian sample

The National Adult Reading Test (NART: Nelson, 1982; Nelson & Willison, 1991) is the most commonly used method for estimating premorbid intelligence in neuropsychological practice and research. It has been used extensively in dementia research (Brayne & Beardsall, 1990; Nelson & O'Connell, 1978) and to a lesser degree in traumatic brain injury (TBI) research (Crawford, Parker & Besson, 1988a). Recent findings suggest NART scores may be sensitive to TBI (Riley & Simmonds, 2003), although available studies are limited by small, mixed injury severity samples and ill-defined severity criteria and assessment time post-injury. Concerns have also been raised regarding the applicability of the NART for Australians as it was developed with a British sample. The Australian National Adult Reading Test (AUSNART: Hennessey & McKenzie, 1994) was developed to address these concerns; however norms were small and limited to Psychology Undergraduate students. There is no published research examining AUSNART in an Australian TBI population. The aims of the current research were to examine the effects of TBI on NART and AUSNART performance, investigate the influence of demographic variables and compare performance on the two tests. Participants were from a large TBI population study and a longitudinal repeated measures design was implemented. Study 1 examined the NART performance of 194 participants at 1, 6 and 12 months post-injury. A significant reduction in NART error score was observed by 6 months post-injury, indicating NART scores are sensitive to TBI. A highly significant effect of education was also noted, with higher level of education providing protection from NART 'impairment'. Age, socio-economic status (SES) and TBI severity also significantly influenced NART scores. Study 2 examined AUSNART performance of 92 participants and was found to be less sensitive to TBI than NART. There was no significant change in AUSNART performance at 6 months, though a significant reduction in error score was noted by 12 months. Age, severity and SES did not significantly affect AUSNART performance but education remained highly influential. AUSNART produced significantly higher estimates of IQ than NART. Study 3 examined two methods for predicting NART performance following TBI: a Multiple Regression equation using initial NART score and a mean NART change score method based on education and age. Tables are provided for each method to assist clinicians. Overall, the results indicate caution is necessary when using the NART to estimate premorbid IQ in an Australian TBI population. AUSNART may eventually provide a more valid estimate than NART, although larger normative studies are required before it can be used with confidence.