Miracle-dz/UniFAR-FTUs huggingface dataset:
Genomic Minimalism in the Early Diverging Intestinal Parasite Giardia lamblia

The genome of the eukaryotic protist Giardia lamblia, an important human intestinal parasite, is compact in structure and content, contains few introns or mitochondrial relics, and has simplified machinery for DNA replication, transcription, RNA processing, and most metabolic pathways. Protein kinases comprise the single largest protein class and reflect Giardia's requirement for a complex signal transduction network for coordinating differentiation. Lateral gene transfer from bacterial and archaeal donors has shaped Giardia's genome, and previously unknown gene families, for example, cysteine-rich structural proteins, have been discovered. Unexpectedly, the genome shows little evidence of heterozygosity, supporting recent speculations that this organism is sexual. This genome sequence will not only be valuable for investigating the evolution of eukaryotes, but will also be applied to the search for new therapeutics for this parasite.
26.2 A 5.5fJ/conv-step 6.4MS/S 13b SAR ADC utilizing a redundancy-facilitated background error-detection-and-correction scheme

Wireless standards, e.g., 802.15. 4g, need high-resolution ADCs (>10b) with very low power and MS/s sampling rates. The SAR ADC is well known for its excellent power efficiency. However, its intrinsic accuracy (DAC matching) is limited up to 10 to 12b in modern CMOS technologies [1]. Scaling up the device dimensions can improve matching but it deteriorates power-efficiency and speed. Alternatively, calibrations [2-5] are introduced to correct errors (e.g., comparator offset and capacitor mismatch) and push the SNDR beyond 62dB. However, most of the calibrations [2-4] are implemented off-chip and the power for the calibration circuit is relatively high when implemented on-chip. Foreground calibration [4-5] is an alternative but is sensitive to environmental changes. We report a low-power fully automated on-chip background calibration that uses a redundancy-facilitated error-detection-and-correction scheme. Thanks to the low-power calibration, this ADC achieves an ENOB of 10.4b and a power efficiency of 5.5fJ/conv-step at 6.4MS/S.
The company that words keep: comparing the statistical structure of child- versus adult-directed language*

ABSTRACT Does child-directed language differ from adult-directed language in ways that might facilitate word learning? Associative structure (the probability that a word appears with its free associates), contextual diversity, word repetitions and frequency were compared longitudinally across six language corpora, with four corpora of language directed at children aged 1 ; 0 to 5 ; 0, and two adult-directed corpora representing spoken and written language. Statistics were adjusted relative to shuffled corpora. Child-directed language was found to be more associative, repetitive and consistent than adult-directed language. Moreover, these statistical properties of child-directed language better predicted word acquisition than the same statistics in adult-directed language. Word frequency and repetitions were the best predictors within word classes (nouns, verbs, adjectives and function words). For all word classes combined, associative structure, contextual diversity and word repetitions best predicted language acquisition. These results support the hypothesis that child-directed language is structured in ways that facilitate language acquisition.
Identification and Characterization of hPEM-2, a Guanine Nucleotide Exchange Factor Specific for Cdc42*

Guanine nucleotide exchange factors of the Dbl family regulate the actin cytoskeleton through activation of Rho-like GTPases. At present the Dbl family consists of more than thirty members; many have not been phenotypically or biochemically characterized. Guanine nucleotide exchange factors universally feature a Dbl homology domain followed by a pleckstrin homology domain. Employing data base screening we identified a recently cloned cDNA, KIAA0424, showing substantial sequence homology with Rac activators such as Tiam1, Sos, Vav, and PIX within the catalytic domain. This cDNA appears to be the human homologue of the Ascidian protein Posterior End Mark-2 (PEM-2). We refer to this exchanger as hPEM-2. hPEM-2 encodes a protein of 70 kDa and features an N-terminal src homology 3 domain, followed by tandem Dbl homology and pleckstrin homology domains. The gene is highly expressed in brain and is localized on the human X-chromosome. Employing biochemical activity assays for Rho-like GTPases we found that hPEM-2 specifically activates Cdc42 and not Rac or RhoA. Ectopic expression of hPEM-2 in NIH3T3 fibroblasts revealed a Cdc42 phenotype featuring filopodia formation, followed by cortical actin polymerization and cell rounding. hPEM-2 represents an exchange factor, which may have a role in the regulation of a number of cellular processes through Cdc42.
Transoral Robotic Surgery in Oropharyngeal Carcinoma.

CONTEXT The incidence of oropharyngeal squamous cell carcinoma has increased during the past decade and is related primarily to the human papillomavirus. This change in etiology, from tobacco and alcohol to human papillomavirus, has resulted in improved survival for the disease. In the United States, open resection had largely been replaced by concurrent chemotherapy and/or radiotherapy by the early 2000s. The advent of transoral surgery has led to an increase in surgery as the primary treatment for both early- and advanced-stage oropharyngeal squamous cell carcinoma because it has potential advantages over open surgery and nonsurgical modalities. OBJECTIVE To provide an overview of transoral robotic surgery for oropharyngeal squamous cell carcinoma and contrast it with other surgical and nonsurgical modalities. DATA SOURCES Articles from 2000 to 2014 were accessioned on PubMed and reviewed for utility by the primary authors. CONCLUSIONS Transoral surgery has become more commonly used as a minimally invasive approach to treat oropharyngeal tumors. Other strategies, including radiation, chemotherapy with radiation, and open surgery, are still important treatment approaches. The treatment options for an individual patient rely on multiple factors, including the tumor location and size, features of the tumor, and patient comorbidities. The continued study of these techniques is important to match the patient with the most appropriate treatment.
Unresectable pancreatic ductal adenocarcinoma in the remnant pancreas diagnosed during every-6-month surveillance after resection of branch duct intraductal papillary mucinous neoplasm: a case report.

CONTEXT There are few studies regarding the surveillance period and interval of resected or observed branch duct intraductal papillary mucinous neoplasms (IPMNs) of the pancreas in terms of early detection of concomitant pancreatic ductal adenocarcinoma. Despite a strict surveillance protocol, some patients are diagnosed with metastatic distinct ductal adenocarcinoma after resection of IPMN. CASE REPORT We herein report a patient with unresectable pancreatic ductal adenocarcinoma that developed in the remnant pancreas 18 months after resection of branch duct IPMN. Although the patient was surveyed every 6 months after the operation and imaging studies at 6 and 12 months postoperatively demonstrated no evidence of recurrence, invasive ductal adenocarcinoma with liver metastasis appeared 18 months after the operation. The patient subsequently underwent chemotherapy; however, he died 9 months after the diagnosis of metachronous pancreatic ductal adenocarcinoma. CONCLUSIONS In some patients with branch duct IPMNs, 6-month surveillance seems to be insufficient to detect resectable concomitant pancreatic ductal adenocarcinoma. Therefore, identification of high-risk patients who require surveillance at shorter intervals is urgently needed.
Robustification of iterative learning control and repetitive control by averaging

This paper describes a recently developed averaging technique to robustify iterative learning and repetitive controllers. The robustified controllers are found by minimising cost functions that are averaged over either multiple analytical time-domain models or experimental frequency-domain data. The aim is to produce a technique that is simple and general, and can be applied to any iterative learning control (ILC) or repetitive control (RC) design that involves the minimisation of a cost function. Substantial improvement in convergence to zero tracking error in the presence of model uncertainties has been observed for both ILC and RC by this averaging technique.
A comparison of the performance of 20 pulse oximeters under conditions of poor perfusion

The performance of 20 pulse oximeters with finger probes was evaluated by comparison of their readings with directly measured arterial blood oxygen saturations. The samples were taken from patients who had undergone cardiac surgery under hypothermic cardiopulmonary bypass and had poor peripheral perfusion. The mean difference (bias, accuracy), standard deviation (precision) and drop‐out rate for each pulse oximeter was determined. An overall ranking of performance of each pulse oximeter was calculated using five criteria (accuracy, precision, number of readings within 3% of standard, percentage of readings given within 3% of standard, expectedoverread limit in 95% of cases). Two pulse oximeters achieved a combination of accuracy and precision such that 95% of measurements would be expected to be within 4% of the co‐oximeter value; these two also had the lowest dropout rate.
Ecological Studies of Legionella Species

The occurrence and viable counts of Legionella pneumophila in acid‐treated water samples of 62 cooling towers on the main island of Japan were determined by inoculating them onto plates of Wadowsky‐Yee‐Okuda (WYO) agar medium. WYO plate cultures of 39 (63%) of the samples yielded L. pneumophila with viable counts ranging from 10 to 104 colony‐forming units per 100 ml.
Borrelia burgdorferi antigens that are targeted by antibody-dependent, complement-mediated killing in the rhesus monkey

We identified surface antigens of Borrelia burgdorferi that are targeted by antibody-dependent, complement-mediated killing (ADCK) in the rhesus monkey. For this purpose, we had available serum samples from three animals infected with B. burgdorferi JD1 by needle inoculation and from two monkeys that were infected with the same B. burgdorferi strain by Ixodes scapularis tick bite. Sera from monkeys from the first group contained antibodies to OspA and OspB detectable by Western blot (immunoblot) using whole B. burgdorferi antigens, whereas serum samples from animals in the second group did not. The targeting of OspA and OspB by functional antibodies was demonstrated directly by showing that ADCK was partially inhibited when antibodies were preincubated with an excess of soluble recombinant OspA or OspB. Simultaneous addition of OspA and OspB did not result in an additive inhibitory effect on ADCK, a result that suggests that the epitopes on OspA and that on OspB targeted by antibody in this mechanism are the same, or at least cross-reacting. The targeting of non-OspA, non-OspB surface antigens was inferred from the fact that sera from tick-inoculated animals, which did not contain detectable anti-OspA or anti-OspB antibodies, were able to effect ADCK. This killing effect was not inhibitable by the addition of recombinant OspA or OspB or both proteins together. We also showed that both immunoglobulin G and M antibodies participate in the ADCK mechanism in the rhesus monkey. Rhesus complement does not kill B. burgdorferi in vitro in the absence of antibody, and antibody alone is effective in killing only at serum dilutions lower than 1:15. However, such "complement-independent" antibodies were not present in all bleeds. Two main conclusions may be drawn from the analysis of our results. First, both OspA and OspB are targeted by the ADCK mechanism in the rhesus monkey. Second, one or more B. burgdorferi surface antigens that are neither OspA nor OspB also participate in ADCK.
Chronic bupropion attenuated the anhedonic component of nicotine withdrawal in rats via inhibition of dopamine reuptake in the nucleus accumbens shell

Bupropion, a dopamine reuptake inhibitor, is an effective therapy for smoking cessation, but the behavioral and neurochemical mechanisms mediating its antismoking properties are relatively unknown. To explore the hypothesis that bupropion ameliorates nicotine withdrawal partly by a dopamine‐dependent mechanism, we investigated the effects of chronic bupropion on potassium‐stimulated dopamine overflow in the nucleus accumbens shell in nicotine‐withdrawing rats. We also assessed the effects of chronic bupropion on behavioral aspects of nicotine withdrawal measured by elevations in brain reward thresholds and somatic signs of withdrawal. Rats were treated with nicotine or saline for 7 days and then coadministration of bupropion or saline was initiated. After 14 days of coadministration of bupropion/saline and nicotine/saline, nicotine/saline administration was terminated, whereas bupropion/saline administration continued. These conditions mimic bupropion administration in human smokers. Cessation of nicotine administration in non‐bupropion‐treated rats elevated reward thresholds reflecting a reward deficit, increased somatic signs and diminished potassium‐evoked dopamine overflow in the nucleus accumbens shell. Chronic bupropion lowered reward thresholds and increased potassium‐evoked dopamine release regardless of previous nicotine exposure, possibly by inhibition of dopamine reuptake, and thus attenuated the anhedonic and neurochemical effects of nicotine withdrawal. Chronic bupropion blocked withdrawal‐associated increased somatic signs. Finally, acute experimenter‐administered nicotine enhanced brain reward function equally in all groups, indicating that bupropion does not alter the reward‐facilitating effects of experimenter‐administered nicotine. In conclusion, the bupropion‐induced increase in extracellular dopamine in the nucleus accumbens shell may ameliorate the anhedonia associated with nicotine withdrawal, which in turn may facilitate smoking cessation.
Intron Retention and TE Exonization Events in ZRANB2

The Zinc finger, RAN-binding domain-containing protein 2 (ZRANB2), contains arginine/serine-rich (RS) domains that mediate its function in the regulation of alternative splicing. The ZRANB2 gene contains 2 LINE elements (L3b, Plat_L3) between the 9th and 10th exons. We identified the exonization event of a LINE element (Plat_L3). Using genomic PCR, RT-PCR amplification, and sequencing of primate DNA and RNA samples, we analyzed the evolutionary features of ZRANB2 transcripts. The results indicated that 2 of the LINE elements were integrated in human and all of the tested primate samples (hominoids: 3 species; Old World monkey: 8 species; New World monkey: 6 species; prosimian: 1 species). Human, rhesus monkey, crab-eating monkey, African-green monkey, and marmoset harbor the exon derived from LINE element (Plat_L3). RT-PCR amplification revealed the long transcripts and their differential expression patterns. Intriguingly, these long transcripts were abundantly expressed in Old World monkey lineages (rhesus, crab-eating, and African-green monkeys) and were expressed via intron retention (IR). Thus, the ZRANB2 gene produces 3 transcript variants in which the Cterminus varies by transposable elements (TEs) exonization and IR mechanisms. Therefore, ZRANB2 is valuable for investigating the evolutionary mechanisms of TE exonization and IR during primate evolution.
The Organization, Promoter Analysis, and Expression of the Human PPARγ Gene*

PPARγ is a member of the PPAR subfamily of nuclear receptors. In this work, the structure of the human PPARγ cDNA and gene was determined, and its promoters and tissue-specific expression were functionally characterized. Similar to the mouse, two PPAR isoforms, PPARγ1 and PPARγ2, were detected in man. The relative expression of human PPARγ was studied by a newly developed and sensitive reverse transcriptase-competitive polymerase chain reaction method, which allowed us to distinguish between PPARγ1 and γ2 mRNA. In all tissues analyzed, PPARγ2 was much less abundant than PPARγ1. Adipose tissue and large intestine have the highest levels of PPARγ mRNA; kidney, liver, and small intestine have intermediate levels; whereas PPARγ is barely detectable in muscle. This high level expression of PPARγ in colon warrants further study in view of the well established role of fatty acid and arachidonic acid derivatives in colonic disease. Similarly as mouse PPARγs, the human PPARγs are activated by thiazolidinediones and prostaglandin J and bind with high affinity to a PPRE. The human PPARγ gene has nine exons and extends over more than 100 kilobases of genomic DNA. Alternate transcription start sites and alternate splicing generate the PPARγ1 and PPARγ2 mRNAs, which differ at their 5′-ends. PPARγ1 is encoded by eight exons, and PPARγ2 is encoded by seven exons. The 5′-untranslated sequence of PPARγ1 is comprised of exons A1 and A2, whereas that of PPARγ2 plus the additional PPARγ2-specific N-terminal amino acids are encoded by exon B, located between exons A2 and A1. The remaining six exons, termed 1 to 6, are common to the PPARγ1 and γ2. Knowledge of the gene structure will allow screening for PPARγ mutations in humans with metabolic disorders, whereas knowledge of its expression pattern and factors regulating its expression could be of major importance in understanding its biology.
Identification of Shigella flexneri isolates carrying the Shiga toxin 1-producing gene in Quebec, Canada, linked to travel to Haiti.

Shiga toxins (Stx1 and Stx2, also called verocytotoxins) are commonly associated with Shiga toxin-producing Escherichia coli (STEC) and Shigella dysenteriae type 1 (Tesh and O’Brien 1991). Recent studies have documented cases of stx carriage in other Shigella species, including S. sonnei linked to travel to Morocco (Nyholm et al. 2015) and S. flexneri with travel history to Caribbean (Gray et al. 2014, 2015). In the province of Quebec, more than 40% of Shigellosis cases are travel-related (Trepanier et al. 2014). Therefore, a retrospective laboratory study was performed by the Laboratoire de sante publique du Quebec to assess the presence of stx gene among the 210 strains of Shigella isolated between 2013 and 2014. The collection included 131 S. sonnei ,7 5S. flexneri ,3 S. boydii, and 1 S. dysenteriae type 12. Polymerase chain reaction targeting genes stx1 and stx2 was performed according to the methods of Paton and Paton (1998). Three isolates of S. flexneri isolated from stool were positive for the stx1 gene and belonged to serotype 2a (n = 2) and serotype y (n = 1). The amplified fragments were sequenced and identity was confirmed. Cases of shigellosis are systematically investigated as provincial regulations of notifiable diseases permits. The first case was a 62-year-old man of Haitian origin living in Montreal (isolate ID 123699). He was admitted to a hospital for bloody diarrhea, fever, and abdominal pain. Empirical antimicrobial treatment with ciprofloxacin was prescribed and the patient was discharged 2 days after admission. The second case was a 55-year-old man of Haitian origin living in Montreal (isolate ID 132104). Ciprofloxacin was prescribed in an outpatient clinic, where he consulted for bloody diarrhea, fever, and abdominal
Real time tracking for enhanced tennis broadcasts

This paper develops real time tracking technology for sports broadcast applications. The specific sport chosen here is the game of tennis. The outputs of the tennis tracking system are spatio-temporal trajectories of motion of the players and the ball which can in turn provide a number of statistics about the game. For instance, the distance travelled by a player, the speed and the acceleration at any instant, as well as court coverage patterns can be obtained from the trajectories. The statistics so obtained can be visualized in compelling ways to enhance the appreciation of the athleticism and strategy involved in the sport. We present techniques for tracking the players and the ball in video obtained from stationary cameras. The problem is challenging as the tracking needs to be performed outdoors, players are fast-moving non-rigid objects, and the ball is a small object that can move at speeds in the range of 150 miles an hour. Player trajectories are obtained by dynamically clustering tracks of local features. Ball segmentation and tracking is based on shape and color features of the ball. Real time tracking results are presented on video recorded live by the authors in an international tennis tournament.
MEPE Activated by Furin Promotes Pulpal Cell Adhesion

Matrix extracellular phosphoglycoprotein (MEPE) is predominantly expressed in osteoblasts, osteocytes, and odontoblasts and plays key biological roles in bone and dentin metabolism. Post-translational modifications are essential for its activation. This study tested the hypothesis that MEPE is activated through proteolytic processing by furin in dental pulp. MEPE was present in three sizes, 1 full-length and 2 cleaved fragments; the cleavage site was 146R↓147. The proprotein convertase family, particularly furin, was a candidate enzyme. Introducing a substitution at the cleavage site inhibited hydrolysis, but there was no cleavage of MEPE expressed in furin-deficient LoVo cells. Therefore, furin is a strong candidate for the proteolytic cleavage of MEPE. The C-terminal cleavage product promoted cell adhesion via its RGD motif. These results indicate that proteolytic processing by furin may activate MEPE during its secretion from odontoblasts and may play important roles in dentinogenesis and pulpal homeostasis. Abbreviations: MEPE, matrix extracellular phosphoglycoprotein; PTM, post-translational modifications; OLC, odontoblast-lineage cells.