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Brandon Phillips added a two-run shot to extend his recent hitting tear and the NL Central leaders followed up a three-game sweep of intrastate rival Cleveland by winning the series opener at Citi Field, a nice present for manager Dusty Baker on his 63rd birthday.
Arroyo, who was 0-3 in six starts since beating Milwaukee on May 7, found his form against one of his favorite opponents. The right-hander entered 7-2 with a 2.81 ERA and three complete games in his previous 12 starts against the Mets - with five other outings that lasted eight innings.
This time, Arroyo (3-4) was pulled in the seventh after giving up Kirk Nieuwenhuis' third homer in two games and a two-run drive by Scott Hairston. Using his usual array of slow breaking balls and odd angles, Arroyo yielded four hits while striking out five and walking two.
Wilson Valdez, making his first major league start in center field, had a two-run double and three RBIs for Cincinnati. Jose Arredondo, Sean Marshall and Aroldis Chapman each worked a hitless inning out of the bullpen.
Reds slugger Joey Votto and Mets star David Wright were both hit by pitches, but neither led to any trouble.
New York starter Dillon Gee (4-5) gave up four runs - three earned - and five hits in six innings. The Mets had just returned from Tampa Bay, where they outscored the Rays 29-9 for a three-game sweep that salvaged a 4-5 road trip against three of baseball's top teams.
Bay was injured when he crashed into the wall while trying to catch Bruce's inside-the-park homer. The Mets said he left the game with a possible concussion, the latest setback for a player who has been an injury-plagued bust in New York since signing a $66 million, four-year contract before the 2010 season.
Bay missed the final two months of his first season with the Mets because of a concussion he sustained while slamming into the left-field fence to make a catch at Dodger Stadium.
Bruce led off the second inning with an opposite-field drive into the left-field corner. Bay raced back, tumbled to the warning track as the ball barely eluded him and then hit his head against the lower part of the fence.
Bay, recently activated from the disabled list, struggled to get to his feet and find the ball. He finally fired it toward the infield, but Bruce slid across the plate to easily beat the relay.
It was Cincinnati's first inside-the-park homer since Drew Stubbs hit one against Toronto on June 17, 2011. The previous inside-the-park shot against the Mets was hit by Blake DeWitt of the Dodgers in Los Angeles on May 6, 2008.
Mets manager Terry Collins and trainer Ray Ramirez came out to check on Bay, who limped slightly as he walked off the field with Ramirez. Third baseman David Wright patted Bay on the head.
Hairston took over in left field. Moments later, he bobbled Ryan Ludwick's double down the left-field line for an error that allowed a run to score.
Bay is batting .187 with four home runs and six RBIs. He was on the disabled list from April 24 until June 6 with a broken rib and is 2 for 25 with a home run since being activated.
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